************************************************************************
********** REPORT OF PROTEIN ANALYSIS  by the WHAT IF program **********
************************************************************************

Date : 2024-11-23
This report was created by WHAT IF version WHATCHECK15.0

This document is a WHAT_CHECK 14.0 report for a PDB-file. Each reported
fact has an assigned severity, one of:

error  : Items marked as errors are considered severe problems requiring
         immediate attention.
warning: Either less severe problems or uncommon structural features. These
         still need special attention.
note   : Statistical values, plots, or other verbose results of tests and
         analyses that have been performed.

If alternate conformations are present, only the first is evaluated. Hydrogen
atoms are only included if explicitly requested, and even then they are not
used in all checks. The software functions less well for non-canonical amino
acids and exotic ligands than for the 20 canonical residues and canonical
nucleic acids.

Some remarks regarding the output:

Residues/atoms in tables are normally given in a few parts:

A number. This is the internal sequence number of the residue used by WHAT IF.
    The first residues in the file get number 1, 2, etc.
The residue type. Normally this is a three letter amino acid type.
The sequence number, between brackets. This is the residue number as it was
    given in the input file. It can be followed by the insertion code.
The chain identifier. A single character. If no chain identifier was given in
    the input file, this will be a minus sign or a blank.
A model number. If no model number exists, like in most X-ray files, this will
    be a blank or occasionally a minus sign.
In case an atom is part of the output, the atom will be listed using the PDB
    nomenclature for type and identifier.

To indicate the normality of a score, the score may be expressed as a Z-value
   or Z-score. This is just the number of standard deviations that the score
   deviates from the expected value. A property of Z-values is that the
   root-mean-square of a group of Z-values (the RMS Z-value) is expected to be
   1.0. Z-values above 4.0 and below -4.0 are very uncommon. If a Z-score is
   used in WHAT IF, the accompanying text will explain how the expected value
   and standard deviation were obtained.
The names of nucleic acids are DGUA, DTHY, OCYT, OADE, etc. The first character
   is a D or O for DNA or RNA respectively. This circumvents ambiguities in the
   many old PDB files in which DNA and RNA were both called A, C, G, and T.



=========================================
==== Compound code /zata/tempdir/5foa/wctemp_besttls/5foa_besttls.pd====
=========================================
 
# 1 # Note: Introduction
WHAT CHECK needs to read a PDB file before it can check it. It does a
series of checks upon reading the file. The results of these checks are
reported in this section (section 2.1). The rest of the report will be more
systematic in that section 2.2 reports on administrative problems. Section
2.3 gives descriptive output that is not directly validating things but
more telling you how WHAT CHECK interpreted the input file. Section 2.4
looks at B-factors, occupancies, and the presence/absence of (spurious)
atoms. Section 2.5 deals with nomenclature problems. Section 2.6 deals with
geometric problems like bond lengths and bond angles. Section 2.7 deals with
torsion angle issues. Section 2.8 looks at atomic clashes. Section 2.9 deals
with packing, accessibility, etc, issues. Section 2.10 deals with hydrogen
bonds, ion packing, and other things that can be summarized under the common
name charge-charge interactions. Section 2.11 gives a summary of whole report
and tells you (if applicable) which symmetry matrices were used. Section 2.12
tells the crystallographer which are the things most in need of manual
correction. And the last section, section 2.13, lists all residues sorted
by their need for visual inspection in light of the electron density.
 
# 2 # Warning: Nonstandard space group setting
The space group name given represents a non-standard setting.
 
Space group name: P 21 2 21
 
Conventional space group : P 21 21 2
WARNING. Date error on HEADER card:
HEADER                                                        5FOA
 
# 3 # Note: Header records from PDB file
Header records from PDB file.
 
HEADER                                                        5FOA
 
# 4 # Error: Missing unit cell information
No SCALE matrix is given in the PDB file.
 
# 5 # Note: Proposal for corrected SCALE matrix
A corrected SCALE matrix has been derived.
 
Proposed scale matrix
  0.008516  0.000000  0.000000
  0.000000  0.007024  0.000000
  0.000000  0.000000  0.003089
 
# 6 # Note: No strange inter-chain connections detected
No covalent bonds have been detected between molecules with non-identical
chain identifiers.
 
# 7 # Note: No duplicate atom names in ligands
All atom names in ligands (if any) seem adequately unique.
 
# 8 # Note: In all cases the primary alternate atom was used
WHAT CHECK saw no need to make any alternate atom corrections (which means
they either are all correct, or there are none).
 
# 9 # Note: No residues detected inside ligands
Either this structure does not contain ligands with amino acid groups inside
it, or their naming is proper (enough).
 
# 10 # Note: No attached groups interfere with hydrogen bond calculations
It seems there are no sugars, lipids, etc., bound (or very close) to atoms
that otherwise could form hydrogen bonds.
 
# 11 # Note: No probable side chain atoms with zero occupancy detected.
Either there are no side chain atoms with zero occupancy, or the side chain
atoms with zero occupancy were not present in the input PDB file (in which
case they are listed as missing atoms), or their positions are sufficiently
improbable to warrant a zero occupancy.
 
# 12 # Note: No probable backbone atoms with zero occupancy detected.
Either there are no backbone atoms with zero occupancy, or the backbone
atoms with zero occupancy were left out of the input PDB file (in
which case they are listed as missing atoms), or their positions are
sufficiently improbable to warrant a zero occupancy.
 
# 13 # Note: All residues have a complete backbone.
No residues have missing backbone atoms.
 
# 14 # Note: No C-alpha only residues
There are no residues that consist of only an alpha carbon atom.
 
# 15 # Note: Content of the PDB file as interpreted by WHAT CHECK
Content of the PDB file as interpreted by WHAT CHECK.
WHAT CHECK has read your PDB file, and stored it internally in what is called
'the soup'. The content of this soup is listed here. An extensive explanation
of all frequently used WHAT CHECK output formats can be found at
swift.cmbi.ru.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
 
     1     1 (   23)   642 (  664) A Protein             /zata/tempdir/5fo...
     2   643 (  752)  1262 ( 1371) B Protein             /zata/tempdir/5fo...
     3  1263 ( 1382)  1544 ( 1663) B Protein             /zata/tempdir/5fo...
     4  1545 (   23)  2186 (  664) C Protein             /zata/tempdir/5fo...
     5  2187 (  752)  2806 ( 1371) D Protein             /zata/tempdir/5fo...
     6  2807 ( 1382)  3088 ( 1663) D Protein             /zata/tempdir/5fo...
     7  3089 (   97)  3277 (  285) E Protein             /zata/tempdir/5fo...
     8  3278 (   97)  3466 (  285) F Protein             /zata/tempdir/5fo...
     9  3467 ( 1663)  3467 ( 1663) B N O2 <-  1544       /zata/tempdir/5fo...
    10  3468 ( 1663)  3468 ( 1663) D N O2 <-  3088       /zata/tempdir/5fo...
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 3466
of which 22 have poor or (essentially) missing atoms
No nucleic acids observed in input file
No sugars recognized in input file
No water observed in input file
Residue numbers increase monotonously OK
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 16 # Note: Ramachandran plot
In this Ramachandran plot x-signs represent glycines, squares represent
prolines, and plus-signs represent the other residues. If too many
plus-signs fall outside the contoured areas then the molecule is poorly
refined (or worse). Proline can only occur in the narrow region around
phi=-60 that also falls within the other contour islands.
 
In a colour picture, the residues that are part of a helix are shown in blue,
strand residues in red. Preferred regions for helical residues are drawn in
blue, for strand residues in red, and for all other residues in green. A full
explanation of the Ramachandran plot together with a series of examples can
be found at the WHAT CHECK website [REF].
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 17 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 18 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 19 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 20 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 21 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 22 # Note: Secondary structure
This is the secondary structure according to DSSP. Only helix (H), overwound
or 3/10-helix (3), strand (S), turn (T) and coil (blank) are shown [REF].
All DSSP related information can be found at swift.cmbi.ru.nl/gv/dssp/
This is not really a structure validation option, but a very scattered
secondary structure (i.e. many strands of only a few residues length, many
Ts inside helices, etc) tends to indicate a poor structure. A full
explanation of the DSSP secondary structure determination program together
with a series of examples can be found at the WHAT CHECK website [REF].
 
Secondary structure assignment
                     10        20        30        40        50        60
                      |         |         |         |         |         |
    1 -   60 SPMYSIITPNILRLESEETMVLEAHDAQGDVPVTVTVHDFPGKKLVLSSEKTVLTPATNH
(  23)-(  82)
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 MGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKVVLVSLQSGYLFIQTDKTIYTPG
(  83)-( 142)
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 STVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDSLSSQNQLGVLPLSWDIPELVNMG
( 143)-( 202)
                    190       200       210       220       230       240
                      |         |         |         |         |         |
  181 -  240 QWKIRAYYENSPQQVFSTEFEVKEYVLPSFEVIVEPTEKFYYIYNEKGLEVTITARFLYG
( 203)-( 262)
                    250       260       270       280       290       300
                      |         |         |         |         |         |
  241 -  300 KKVEGTAFVIFGIQDGEQRISLPESLKRIPIEDGSGEVVLSRKVLLDGVQNPRAEDLVGK
( 263)-( 322)
                    310       320       330       340       350       360
                      |         |         |         |         |         |
  301 -  360 SLYVSATVILHSGSDMVQAERSGIPIVTSPYQIHFTKTPKYFKPGMPFDLMVFVTNPDGS
( 323)-( 382)
                    370       380       390       400       410       420
                      |         |         |         |         |         |
  361 -  420 PAYRVPVAVQGEDTVQSLTQGDGVAKLSINTHPSQKPLSITVRTKKQELSEAEQATRTMQ
( 383)-( 442)
                    430       440       450       460       470       480
                      |         |         |         |         |         |
  421 -  480 ALPYSTVGNSNNYLHLSVLRTELRPGETLNVNFLLRMDRAHEAKIRYYTYLIMNKGRLLK
( 443)-( 502)
                    490       500       510       520       530       540
                      |         |         |         |         |         |
  481 -  540 AGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYTLIGASGQREVVADSVWVDVKDSCVGS
( 503)-( 562)
                    550       560       570       580       590       600
                      |         |         |         |         |         |
  541 -  600 LVVKSGQSEDRQPVPGQQMTLKIEGDHGARVVLVAVDKGVFVLNKKNKLTQSKIWDVVEK
( 563)-( 622)
                    610       620       630       640
                      |         |         |         |
  601 -  642 ADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAELQCPQ
( 623)-( 664)
                  650       660       670       680       690       700
                    |         |         |         |         |         |
  643 -  702 DEDIIAEENIVSRSEFPESWLWNVEDLKEPPKNGISTKLMNIFLKDSITTWEILAVSMSD
( 752)-( 811)
                  710       720       730       740       750       760
                    |         |         |         |         |         |
  703 -  762 KKGICVADPFEVTVMQDFFIDLRLPYSVVRNEQVEIRAVLYNYRQNQELKVRVELLHNPA
( 812)-( 871)
                  770       780       790       800       810       820
                    |         |         |         |         |         |
  763 -  822 FCSLATTKRRHQQTVTIPPKSSLSVPYVIVPLKTGLQEVEVKAAVYHHFISDGVRKSLKV
( 872)-( 931)
                  830       840       850       860       870       880
                    |         |         |         |         |         |
  823 -  882 VPEGIRMNKTVAVRTLDPERLGREGVQKEDIPPADLSDQVPDTESETRILLQGTPVAQMT
( 932)-( 991)
                  890       900       910       920       930       940
                    |         |         |         |         |         |
  883 -  942 EDAVDAERLKHLIVTPSGCGEENMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIKK
( 992)-(1051)
                  950       960       970       980       990      1000
                    |         |         |         |         |         |
  943 - 1002 GYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILEK
(1052)-(1111)
                 1010      1020      1030      1040      1050      1060
                    |         |         |         |         |         |
 1003 - 1062 QKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSITK
(1112)-(1171)
                 1070      1080      1090      1100      1110      1120
                    |         |         |         |         |         |
 1063 - 1122 AGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNVE
(1172)-(1231)
                 1130      1140      1150      1160      1170      1180
                    |         |         |         |         |         |
 1123 - 1182 ATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPDHQE
(1232)-(1291)
                 1190      1200      1210      1220      1230      1240
                    |         |         |         |         |         |
 1183 - 1242 LNLDVSLQLPSRSSKITHRIHWESASLLRSEETKENEGFTVTAEGKGQGTLSVVTMYHAK
(1292)-(1351)
                 1250      1260
                    |         |
 1243 - 1262 AKDQLTCNKFDLKVTIKPAP
(1352)-(1371)
                 1270      1280      1290      1300      1310      1320
                    |         |         |         |         |         |
 1263 - 1322 NTMILEICTRYRGDQDATMSILDISMMTGFAPDTDDLKQLANGVDRYISKYELDKAFSDR
(1382)-(1441)
                 1330      1340      1350      1360      1370      1380
                    |         |         |         |         |         |
 1323 - 1382 NTLIIYLDKVSHSEDDCLAFKVHQYFNVELIQPGAVKVYAYYNLEESCTRFYHPEKEDGK
(1442)-(1501)
                 1390      1400      1410      1420      1430      1440
                    |         |         |         |         |         |
 1383 - 1442 LNKLCRDELCRCAEENCFIQKSDDKVTLEERLDKACEPGVDYVYKTRLVKVQLSNDFDEY
(1502)-(1561)
                 1450      1460      1470      1480      1490      1500
                    |         |         |         |         |         |
 1443 - 1502 IMAIEQTIKSGSDEVQVGQQRTFISPIKCREALKLEEKKHYLMWGLSSDFWGEKPNLSYI
(1562)-(1621)
                 1510      1520      1530      1540
                    |         |         |         |
 1503 - 1544 IGKDTWVEHWPEEDECQDEENQKQCQDLGAFTESMVVFGCPN
(1622)-(1663)
               1550      1560      1570      1580      1590      1600
                  |         |         |         |         |         |
 1545 - 1604 SPMYSIITPNILRLESEETMVLEAHDAQGDVPVTVTVHDFPGKKLVLSSEKTVLTPATNH
(  23)-(  82)
               1610      1620      1630      1640      1650      1660
                  |         |         |         |         |         |
 1605 - 1664 MGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKVVLVSLQSGYLFIQTDKTIYTPG
(  83)-( 142)
               1670      1680      1690      1700      1710      1720
                  |         |         |         |         |         |
 1665 - 1724 STVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDSLSSQNQLGVLPLSWDIPELVNMG
( 143)-( 202)
               1730      1740      1750      1760      1770      1780
                  |         |         |         |         |         |
 1725 - 1784 QWKIRAYYENSPQQVFSTEFEVKEYVLPSFEVIVEPTEKFYYIYNEKGLEVTITARFLYG
( 203)-( 262)
               1790      1800      1810      1820      1830      1840
                  |         |         |         |         |         |
 1785 - 1844 KKVEGTAFVIFGIQDGEQRISLPESLKRIPIEDGSGEVVLSRKVLLDGVQNPRAEDLVGK
( 263)-( 322)
               1850      1860      1870      1880      1890      1900
                  |         |         |         |         |         |
 1845 - 1904 SLYVSATVILHSGSDMVQAERSGIPIVTSPYQIHFTKTPKYFKPGMPFDLMVFVTNPDGS
( 323)-( 382)
               1910      1920      1930      1940      1950      1960
                  |         |         |         |         |         |
 1905 - 1964 PAYRVPVAVQGEDTVQSLTQGDGVAKLSINTHPSQKPLSITVRTKKQELSEAEQATRTMQ
( 383)-( 442)
               1970      1980      1990      2000      2010      2020
                  |         |         |         |         |         |
 1965 - 2024 ALPYSTVGNSNNYLHLSVLRTELRPGETLNVNFLLRMDRAHEAKIRYYTYLIMNKGRLLK
( 443)-( 502)
               2030      2040      2050      2060      2070      2080
                  |         |         |         |         |         |
 2025 - 2084 AGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYTLIGASGQREVVADSVWVDVKDSCVGS
( 503)-( 562)
               2090      2100      2110      2120      2130      2140
                  |         |         |         |         |         |
 2085 - 2144 LVVKSGQSEDRQPVPGQQMTLKIEGDHGARVVLVAVDKGVFVLNKKNKLTQSKIWDVVEK
( 563)-( 622)
               2150      2160      2170      2180
                  |         |         |         |
 2145 - 2186 ADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAELQCPQ
( 623)-( 664)
             2190      2200      2210      2220      2230      2240
                |         |         |         |         |         |
 2187 - 2246 DEDIIAEENIVSRSEFPESWLWNVEDLKEPPKNGISTKLMNIFLKDSITTWEILAVSMSD
( 752)-( 811)
             2250      2260      2270      2280      2290      2300
                |         |         |         |         |         |
 2247 - 2306 KKGICVADPFEVTVMQDFFIDLRLPYSVVRNEQVEIRAVLYNYRQNQELKVRVELLHNPA
( 812)-( 871)
             2310      2320      2330      2340      2350      2360
                |         |         |         |         |         |
 2307 - 2366 FCSLATTKRRHQQTVTIPPKSSLSVPYVIVPLKTGLQEVEVKAAVYHHFISDGVRKSLKV
( 872)-( 931)
             2370      2380      2390      2400      2410      2420
                |         |         |         |         |         |
 2367 - 2426 VPEGIRMNKTVAVRTLDPERLGREGVQKEDIPPADLSDQVPDTESETRILLQGTPVAQMT
( 932)-( 991)
             2430      2440      2450      2460      2470      2480
                |         |         |         |         |         |
 2427 - 2486 EDAVDAERLKHLIVTPSGCGEENMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIKK
( 992)-(1051)
             2490      2500      2510      2520      2530      2540
                |         |         |         |         |         |
 2487 - 2546 GYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILEK
(1052)-(1111)
             2550      2560      2570      2580      2590      2600
                |         |         |         |         |         |
 2547 - 2606 QKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSITK
(1112)-(1171)
             2610      2620      2630      2640      2650      2660
                |         |         |         |         |         |
 2607 - 2666 AGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNVE
(1172)-(1231)
             2670      2680      2690      2700      2710      2720
                |         |         |         |         |         |
 2667 - 2726 ATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPDHQE
(1232)-(1291)
             2730      2740      2750      2760      2770      2780
                |         |         |         |         |         |
 2727 - 2786 LNLDVSLQLPSRSSKITHRIHWESASLLRSEETKENEGFTVTAEGKGQGTLSVVTMYHAK
(1292)-(1351)
             2790      2800
                |         |
 2787 - 2806 AKDQLTCNKFDLKVTIKPAP
(1352)-(1371)
             2810      2820      2830      2840      2850      2860
                |         |         |         |         |         |
 2807 - 2866 NTMILEICTRYRGDQDATMSILDISMMTGFAPDTDDLKQLANGVDRYISKYELDKAFSDR
(1382)-(1441)
             2870      2880      2890      2900      2910      2920
                |         |         |         |         |         |
 2867 - 2926 NTLIIYLDKVSHSEDDCLAFKVHQYFNVELIQPGAVKVYAYYNLEESCTRFYHPEKEDGK
(1442)-(1501)
             2930      2940      2950      2960      2970      2980
                |         |         |         |         |         |
 2927 - 2986 LNKLCRDELCRCAEENCFIQKSDDKVTLEERLDKACEPGVDYVYKTRLVKVQLSNDFDEY
(1502)-(1561)
             2990      3000      3010      3020      3030      3040
                |         |         |         |         |         |
 2987 - 3046 IMAIEQTIKSGSDEVQVGQQRTFISPIKCREALKLEEKKHYLMWGLSSDFWGEKPNLSYI
(1562)-(1621)
             3050      3060      3070      3080
                |         |         |         |
 3047 - 3088 IGKDTWVEHWPEEDECQDEENQKQCQDLGAFTESMVVFGCPN
(1622)-(1663)
           3090      3100      3110      3120      3130      3140
              |         |         |         |         |         |
 3089 - 3148 SCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVE
(  97)-( 156)
           3150      3160      3170      3180      3190      3200
              |         |         |         |         |         |
 3149 - 3208 FCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDP
( 157)-( 216)
           3210      3220      3230      3240      3250      3260
              |         |         |         |         |         |
 3209 - 3268 LPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEW
( 217)-( 276)
           3270
              |
 3269 - 3277 SGPPPECRG
( 277)-( 285)
            3280      3290      3300      3310      3320      3330
               |         |         |         |         |         |
 3278 - 3337 SCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVE
(  97)-( 156)
            3340      3350      3360      3370      3380      3390
               |         |         |         |         |         |
 3338 - 3397 FCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDP
( 157)-( 216)
            3400      3410      3420      3430      3440      3450
               |         |         |         |         |         |
 3398 - 3457 LPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEW
( 217)-( 276)
            3460
               |
 3458 - 3466 SGPPPECRG
( 277)-( 285)
 
 
 
 
# 23 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
 
# 24 # Note: No artificial side chains detected
No artificial side-chain positions characterized by chi-1=0.0 or chi-1=180.0
have been detected.
 
# 25 # Warning: Missing atoms
The atoms listed in the table below are missing from the entry. If many atoms
are missing, the other checks can become less sensitive. Be aware that it
often happens that groups at the termini of DNA or RNA are really missing,
so that the absence of these atoms normally is neither an error nor the
result of poor electron density. Some of the atoms listed here might also be
listed by other checks, most noticeably by the options in the previous
section that list missing atoms in several categories. The plausible atoms
with zero occupancy are not listed here, as they already got assigned a
non-zero occupancy, and thus are no longer 'missing'.
 
   76 SER  (  98-) A  -    OG
   77 GLU  (  99-) A  -    CG
   77 GLU  (  99-) A  -    CD
   77 GLU  (  99-) A  -    OE1
   77 GLU  (  99-) A  -    OE2
 1178 PRO  (1287-) B  -    CG
 1178 PRO  (1287-) B  -    CD
 1179 ASP  (1288-) B  -    CG
 1179 ASP  (1288-) B  -    OD1
 1179 ASP  (1288-) B  -    OD2
 1180 HIS  (1289-) B  -    CG
 1180 HIS  (1289-) B  -    ND1
 1180 HIS  (1289-) B  -    CD2
 1180 HIS  (1289-) B  -    CE1
 1180 HIS  (1289-) B  -    NE2
And so on for a total of    73 lines.
 
# 26 # Note: All B-factors fall in the range 0.0 - 100.0
All B-factors are larger than zero, and none are observed above 100.0.
 
# 27 # Note: C-terminus capping
The residues listed in the table below are either C-terminal or pseudo
C-terminal (i.e. last residue before a missing residue).
In X-ray the coordinates must be located in density. Mobility or disorder
sometimes cause this density to be so poor that the positions of the atoms
cannot be determined. Crystallographers tend to leave out the atoms in such
cases. In many cases the N- or C-terminal residues are too disordered to see.
In case of the N-terminus, you can often see from the residue numbers if
there are missing residues; at the C-terminus this is impossible. Therefore,
often the position of the backbone nitrogen of the first residue missing
at the C-terminal end is calculated and added to indicate that there
are missing residues. As a single N causes validation trouble, we remove
these single-N-residues before doing the validation. If this happened,
the label -N is added to the pseudo C-terminus. Other labels can be +X
in case something weird is bound to the backbone C, or +OXT if a spurious
OXT atom is found. -OXT indicates that an expected OXT is missing. 'Swap'
means that the O' and O'' (O and OXT in PDB files) have been swapped in
terms of nomenclature. 'Bad' means that something bad happened that WHAT IF
does not understand. In such cases you might get three residue numbers in
square brackets; one of those might be what WHAT IF had expected to find,
but then it also might not). In case of chain breaks the number of missing
residues is listen in round brackets. OK means what it suggests...
 
Be aware that we cannot easily see the difference between these errors and
errors in the chain and residue numbering schemes. So do not blindly trust
the table below. If you get weird errors at, or near, the left-over
incomplete C-terminal residue, please check by hand if a missing Oxt or
a removed single N is the cause. Also, many peptidic ligands get the same
chain identifier as the larger protein they are bound to. In such cases there
are more than one C-termini and OXTs with the same ID. WHAT IF gives some
random warnings about these cases. So, don't take everything at face value,
but think for yourself.
 
  642 GLN  ( 664-) A  -        OK
 1262 PRO  (1371-) B  -        OK (10)
 1544 ASN  (1663-) B  -        +OXT [1544 ; 642 ; 1663]
 2186 GLN  ( 664-) C  -        OK
 2806 PRO  (1371-) D  -        OK (10)
 3088 ASN  (1663-) D  -        +OXT [3088 ; 642 ; 1663]
 3277 GLY  ( 285-) E  -        OK
 3466 GLY  ( 285-) F  -        OK
 
# 28 # Note: Weights administratively correct
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which
makes them administratively correct.
 
# 29 # Note: Normal distribution of occupancy values
 
The distribution of the occupancy values in this file seems 'normal'.
 
Be aware that this evaluation is merely the result of comparing this file
with about 500 well-refined high-resolution files in the PDB. If this file
has much higher or much lower resolution than the PDB files used
in WHAT CHECK's training set, non-normal values might very well be perfectly
fine, or normal values might actually be not so normal. So, this check is
actually more an indicator and certainly not a check in which I have great
confidence.
 
# 30 # Note: All occupancies seem to add up to 0.0 - 1.0.
In principle, the occupancy of all alternates of one atom should add up till
0.0 - 1.0. 0.0 is used for the missing atom (i.e. an atom not seen in the
electron density). Obviously, there is nothing terribly wrong when a few
occupancies add up to a bit more than 1.0, because the mathematics of
refinement allow for that. However, if it happens often, it seems worth
evaluating this in light of the refinement protocol used.
 
# 31 # Warning: What type of B-factor?
WHAT CHECK does not yet know well how to cope with B-factors in case TLS has
been used. It simply assumes that the B-factor listed on the ATOM and HETATM
cards are the total B-factors. When TLS refinement is used that assumption
sometimes is not correct. The header of the PDB file states that TLS groups
were used. So, if WHAT CHECK complains about your  B-factors, while you think
that they are OK, then check for TLS related B-factor problems first.
 
Number of TLS groups mentione in PDB file header: 0
 
Temperature not mentioned in PDB file. This most likely means
that the temperature record is absent.
Room temperature assumed
 
# 32 # Note: Number of buried atoms with low B-factor is OK
For protein structures determined at room temperature, no more than about 1
percent of the B factors of buried atoms is below 5.0. In liquid
nitrogen this percentage is allowed to be higher, of course.
 
Percentage of buried atoms with B less than 5 :   0.00
 
# 33 # Note: B-factor distribution normal
The distribution of B-factors within residues is within expected ranges.
A value over 1.5 here would mean that the B-factors show signs of
over-refinement.
 
RMS Z-score :  0.365 over   24383 bonds
Average difference in B over a bond :    0.00
RMS difference in B over a bond :    0.00
 
# 34 # Warning: B-factor plot useless
All average B-factors are equal. Plot suppressed.
 
Chain identifier: A
 
# 35 # Warning: B-factor plot useless
All average B-factors are equal. Plot suppressed.
 
Chain identifier: B
 
# 36 # Warning: B-factor plot useless
All average B-factors are equal. Plot suppressed.
 
Chain identifier: C
 
# 37 # Warning: B-factor plot useless
All average B-factors are equal. Plot suppressed.
 
Chain identifier: D
 
# 38 # Warning: B-factor plot useless
All average B-factors are equal. Plot suppressed.
 
Chain identifier: E
 
# 39 # Warning: B-factor plot useless
All average B-factors are equal. Plot suppressed.
 
Chain identifier: F
 
# 40 # Note: Introduction to the nomenclature section.
Nomenclature problems seem, at first, rather unimportant. After all who
cares if we call the delta atoms in leucine delta2 and delta1 rather than
the other way around. Chemically speaking that is correct. But structures
have not been solved and deposited just for chemists to look at them. Most
times a structure is used, it is by software in a bioinformatics lab. And
if they compare structures in which the one used C delta1 and delta2 and the
other uses C delta2 and delta1, then that comparison will fail. Also, we
recalculate all structures every so many years to make sure that everybody
always can get access to the best coordinates that can be obtained from
the (your?) experimental data. These recalculations will be troublesome if
there are nomenclature problems.
 
Several nomenclature problems actually are worse than that. At the
WHAT CHECK website [REF] you can get an overview of the importance of all
nomenclature problems that we list.
 
# 41 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.
 
# 42 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.
 
# 43 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.
 
# 44 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.
 
# 45 # Note: Arginine nomenclature OK
No errors were detected in arginine nomenclature.
 
# 46 # Warning: Tyrosine convention problem
The tyrosine residues listed in the table below have their chi-2 not between
-90.0 and 90.0
 
  239 TYR  ( 261-) A  -
 1783 TYR  ( 261-) C  -
 1907 TYR  ( 385-) C  -
 
# 47 # Warning: Phenylalanine convention problem
The phenylalanine residues listed in the table below have their chi-2 not
between -90.0 and 90.0.
 
  251 PHE  ( 273-) A  -
 1009 PHE  (1118-) B  -
 1400 PHE  (1519-) B  -
 2472 PHE  (1037-) D  -
 2553 PHE  (1118-) D  -
 2683 PHE  (1248-) D  -
 2944 PHE  (1519-) D  -
 
# 48 # Note: Aspartic acid torsion conventions OK
No errors were detected in aspartic acid torsion angle conventions.
 
# 49 # Note: Glutamic acid torsion conventions OK
No errors were detected in glutamic acid torsion angle conventions.
 
# 50 # Note: Phosphate group names OK in DNA/RNA
No errors were detected in nucleic acid phosphate group naming conventions
(or this structure contains no nucleic acids).
 
# 51 # Note: Heavy atom naming OK
No errors were detected in the atom names for non-hydrogen atoms. Please
be aware that the PDB wants us to deliberately make some nomenclature errors;
especially in non-canonical amino acids.
 
# 52 # Note: No decreasing residue numbers
All residue numbers are strictly increasing within each chain.
 
# 53 # Warning: Unusual bond lengths
The bond lengths listed in the table below were found to deviate more than 4
sigma from standard bond lengths (both standard values and sigmas for amino
acid residues have been taken from Engh and Huber [REF], for DNA they were
taken from Parkinson et al [REF]). In the table below for each unusual bond
the bond length and the number of standard deviations it differs from the
normal value is given.
 
Atom names starting with "-" belong to the previous residue in the chain. If
the second atom name is "-SG*", the disulphide bridge has a deviating length.
 
 2147 ILE  ( 625-) C  -    CG1  CD1   1.30   -5.6
 2584 ILE  (1149-) D  -    CG1  CD1   1.34   -4.5
 3361 ILE  ( 180-) F  -    CG1  CD1   1.33   -4.7
 
# 54 # Warning: Low bond length variability
Bond lengths were found to deviate less than normal from the mean Engh and
Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS
Z-score given below is expected to be near 1.0 for a normally restrained
data set. The fact that it is lower than 0.667 in this structure might
indicate that too-strong restraints have been used in the refinement. This
can only be a problem  for high resolution X-ray structures.
 
 RMS Z-score for bond lengths: 0.456
 RMS-deviation in bond distances: 0.011
 
# 55 # Note: No bond length directionality
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] values for DNA/RNA does not show
significant systematic deviations.
 
# 56 # Warning: Unusual bond angles
The bond angles listed in the table below were found to deviate more than 4
sigma from standard bond angles (both standard values and sigma for protein
residues have been taken from Engh and Huber [REF], for DNA/RNA from
Parkinson et al [REF]). In the table below for each strange angle the bond
angle and the number of standard deviations it differs from the standard
values is given. Please note that disulphide bridges are neglected. Atoms
starting with "-" belong to the previous residue in the sequence.
 
   39 ASP  (  61-) A  -    CA   CB   CG  117.93    5.3
  113 ASP  ( 135-) A  -    CA   CB   CG  116.68    4.1
  458 ASP  ( 480-) A  -    CA   CB   CG  117.71    5.1
  535 ASP  ( 557-) A  -    CA   CB   CG  117.44    4.8
  619 ASP  ( 641-) A  -    CA   CB   CG  118.35    5.8
  645 ASP  ( 754-) B  -    CA   CB   CG  119.69    7.1
  685 PHE  ( 794-) B  -    CA   CB   CG  109.31   -4.5
  688 ASP  ( 797-) B  -    CA   CB   CG  116.72    4.1
  733 ASN  ( 842-) B  -    CA   CB   CG  121.04    8.4
  830 ASN  ( 939-) B  -    CA   CB   CG  117.31    4.7
  852 ASP  ( 961-) B  -    CA   CB   CG  116.66    4.1
  864 ASP  ( 973-) B  -    CA   CB   CG  120.08    7.5
  887 ASP  ( 996-) B  -    CA   CB   CG  120.13    7.5
  905 ASN  (1014-) B  -    CA   CB   CG  117.32    4.7
 1066 PHE  (1175-) B  -    CA   CB   CG  109.15   -4.7
And so on for a total of    62 lines.
 
# 57 # Note: Normal bond angle variability
Bond angles were found to deviate normally from the mean standard bond angles
(normal values for protein residues were taken from Engh and Huber [REF], for
DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected
to be near 1.0 for a normally restrained data set, and this is indeed
observed for very high resolution X-ray structures.
 
 RMS Z-score for bond angles: 0.745
 RMS-deviation in bond angles: 1.366
 
# 58 # Note: Residue hand check OK
No atoms are observed that have the wrong handedness. Be aware, though, that
WHAT CHECK might have corrected the handedness of some atoms already. The
handedness has not been corrected for any case where the problem is worse
than just an administrative discomfort.
 
# 59 # Note: Chirality OK
All protein atoms have proper chirality, or there is no intact protein
present in the PDB file.
The average deviation= 0.712
 
# 60 # Note: Improper dihedral angle distribution OK
The RMS Z-score for all improper dihedrals in the structure is within normal
ranges.
 
 Improper dihedral RMS Z-score : 0.597
 
# 61 # Note: Tau angles OK
All of the tau angles (N-C-alpha-C) of amino acids fall within expected
RMS deviations.
 
# 62 # Note: Normal tau angle deviations
The RMS Z-score for the tau angles (N-C-alpha-C) in the structure falls
within the normal range that we guess to be 0.5 - 1.5. Be aware, we
determined the tau normal distributions from 500 high-resolution X-ray
structures, rather than from CSD data, so we cannot be 100 percent certain
about these numbers.
 
 Tau angle RMS Z-score : 0.752
 
# 63 # Error: Side chain planarity problems
The side chains of the residues listed in the table below contain a planar
group that was found to deviate from planarity by more than 4.0 times the
expected value. For an amino acid residue that has a side chain with a
planar group, the RMS deviation of the atoms to a least squares plane was
determined. The number in the table is the number of standard deviations
this RMS value deviates from the expected value. Not knowing better yet, we
assume that planarity of the groups analyzed should be perfect.
 
 1194 ARG  (1303-) B  -   4.80
 2916 ARG  (1491-) D  -   4.12
 
# 64 # Note: Atoms connected to aromatic rings OK
All of the atoms that are connected to planar aromatic rings in side chains
of amino-acid residues are in the plane within expected RMS deviations.
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 
# 65 # Error: Ramachandran Z-score very low
The score expressing how well the backbone conformations of all residues
correspond to the known allowed areas in the Ramachandran plot is very low.
 
 Ramachandran Z-score : -4.409
 
# 66 # Note: Ramachandran check
The list contains per-residue Z-scores describing how well each residue
fits into the allowed areas of the Ramachandran plot will not be printed
because WHAT CHECK found no reason to cry.
 
# 67 # Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
torsion angles.
 
These scores give an impression of how `normal' the torsion angles in
protein residues are. All torsion angles except omega are used for
calculating a `normality' score. Average values and standard deviations were
obtained from the residues in the WHAT CHECK database. These are used to
calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a
score of less than -3.0 is worrying. For such residues more than one torsion
angle is in a highly unlikely position.
 
 2235 THR  ( 800-) D  -   -3.5
  691 THR  ( 800-) B  -   -3.4
 1376 PRO  (1495-) B  -   -2.9
 2920 PRO  (1495-) D  -   -2.8
 3293 PRO  ( 112-) F  -   -2.8
 3104 PRO  ( 112-) E  -   -2.8
  505 PRO  ( 527-) A  -   -2.7
 3257 ILE  ( 265-) E  -   -2.7
 2049 PRO  ( 527-) C  -   -2.7
 3416 ILE  ( 235-) F  -   -2.7
  882 THR  ( 991-) B  -   -2.7
  646 ILE  ( 755-) B  -   -2.7
 1340 LEU  (1459-) B  -   -2.6
 2884 LEU  (1459-) D  -   -2.6
 3238 ARG  ( 246-) E  -   -2.6
And so on for a total of   166 lines.
 
# 68 # Warning: Backbone evaluation reveals unusual conformations
The residues listed in the table below have abnormal backbone torsion
angles.
 
Residues with `forbidden' phi-psi combinations are listed, as well as
residues with unusual omega angles (deviating by more than 3 sigma from the
normal value). Please note that it is normal if about 5 percent of the
residues is listed here as having unusual phi-psi combinations.
 
    8 THR  (  30-) A  - Omega to (next) Pro poor
   26 ASP  (  48-) A  - Poor phi/psi
   29 GLY  (  51-) A  - Poor phi/psi
   31 VAL  (  53-) A  - Omega to (next) Pro poor
   40 PHE  (  62-) A  - Omega to (next) Pro poor
   43 LYS  (  65-) A  - Poor phi/psi
   46 VAL  (  68-) A  - omega poor
   55 THR  (  77-) A  - Omega to (next) Pro poor
   68 ILE  (  90-) A  - Omega to (next) Pro poor
   73 GLU  (  95-) A  - omega poor
   76 SER  (  98-) A  - Poor phi/psi, omega poor
   77 GLU  (  99-) A  - omega poor
   79 GLY  ( 101-) A  - Poor phi/psi
   91 GLY  ( 113-) A  - Poor phi/psi
  106 GLY  ( 128-) A  - Poor phi/psi
And so on for a total of   501 lines.
 
# 69 # Error: Chi-1/chi-2 rotamer problems
List of residues with a poor chi-1/chi-2 combination. Be aware that for this
validation option the individual scores are far less important than the
overall score that is given below the table.
 
   14 LEU  (  36-) A  -    -1.32
   22 LEU  (  44-) A  -    -1.32
   45 LEU  (  67-) A  -    -1.32
   54 LEU  (  76-) A  -    -1.32
  100 LEU  ( 122-) A  -    -1.32
  103 LEU  ( 125-) A  -    -1.32
  108 LEU  ( 130-) A  -    -1.32
  164 LEU  ( 186-) A  -    -1.31
  169 LEU  ( 191-) A  -    -1.32
  378 LEU  ( 400-) A  -    -1.31
  409 LEU  ( 431-) A  -    -1.32
  422 LEU  ( 444-) A  -    -1.32
  443 LEU  ( 465-) A  -    -1.32
  449 LEU  ( 471-) A  -    -1.31
  455 LEU  ( 477-) A  -    -1.32
And so on for a total of  1846 lines.
 
# 70 # Error: chi-1/chi-2 angle correlation Z-score very low
The score expressing how well the chi-1/chi-2 angles of all residues
correspond to the populated areas in the database is
very low.
 
 chi-1/chi-2 correlation Z-score : -5.884
 
# 71 # Warning: Unusual rotamers
The residues listed in the table below have a rotamer that is not seen very
often in the database of solved protein structures. This option determines
for every residue the position specific chi-1 rotamer distribution.
Thereafter it verified whether the actual residue in the molecule has the
most preferred rotamer or not. If the actual rotamer is the preferred one,
the score is 1.0. If the actual rotamer is unique, the score is 0.0. If
there are two preferred rotamers, with a population distribution of 3:2 and
your rotamer sits in the lesser populated rotamer, the score will be 0.667.
No value will be given if insufficient hits are found in the database.
 
It is not necessarily an error if a few residues have rotamer values below
0.3, but careful inspection of all residues with these low values could be
worth it.
 
   49 SER  (  71-) A  -   0.35
 3325 THR  ( 144-) F  -   0.35
 3049 LYS  (1624-) D  -   0.36
 1211 ARG  (1320-) B  -   0.36
 1287 SER  (1406-) B  -   0.36
 1593 SER  (  71-) C  -   0.36
 2937 ARG  (1512-) D  -   0.36
 1505 LYS  (1624-) B  -   0.36
 1615 ASN  (  93-) C  -   0.36
 1719 GLU  ( 197-) C  -   0.37
  332 GLN  ( 354-) A  -   0.37
   52 THR  (  74-) A  -   0.38
  388 SER  ( 410-) A  -   0.38
  425 SER  ( 447-) A  -   0.38
 2750 SER  (1315-) D  -   0.38
And so on for a total of    34 lines.
 
# 72 # Warning: Unusual backbone conformations
For the residues listed in the table below, the backbone formed by itself and
two neighbouring residues on either side is in a conformation that is not
seen very often in the database of solved protein structures. The number
given in the table is the number of similar backbone conformations in the
database with the same amino acid in the centre.
 
For this check, backbone conformations are compared with database structures
using C-alpha superpositions with some restraints on the backbone oxygen
positions.
 
A residue mentioned in the table can be part of a strange loop, or there
might be something wrong with it or its directly surrounding residues. There
are a few of these in every protein, but in any case it is worth looking at,
especially if a regular DSSP secondary structure (H or S for helix or strand,
respectively) is indicated!
 
   76 SER  (  98-) A  -       0
   77 GLU  (  99-) A  -       0
   78 LYS  ( 100-) A  -       0
   79 GLY  ( 101-) A  -       0
  179 MET  ( 201-) A  -       0
  209 SER  ( 231-) A  -       0
  408 GLU  ( 430-) A  -       0
  504 ILE  ( 526-) A  -       0
  505 PRO  ( 527-) A  -       0
  519 SER  ( 541-) A  -       0
  609 SER  ( 631-) A  -       0
  664 TRP  ( 773-) B  -       0
  841 GLU  ( 950-) B  -       0
  842 ARG  ( 951-) B  -       0
  843 LEU  ( 952-) B  -       0
And so on for a total of   154 lines.
 
# 73 # Note: Backbone conformation Z-score OK
The backbone conformation analysis gives a score that is normal for well
refined protein structures.
 
 Backbone conformation Z-score : -0.833
 
# 74 # Note: Omega angle restraint OK
The omega angles for trans-peptide bonds in a structure is expected to give a
gaussian distribution with the average around +178 degrees, and a standard
deviation around 5.5. In the current structure the standard deviation agrees
with this expectation.
 
Omega average and std. deviation= 179.360 6.452
 
# 75 # Warning: Unusual PRO puckering amplitudes
The proline residues listed in the table below have a puckering amplitude
that is outside of normal ranges. Puckering parameters were calculated by
the method of Cremer and Pople [REF]. Normal PRO rings have a puckering
amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom
for a PRO residue, this could indicate disorder between the two different
normal ring forms (with C-gamma below and above the ring, respectively). If
Q is higher than 0.45 Angstrom something could have gone wrong during the
refinement. Be aware that this is a warning with a low confidence level. See:
Who checks the checkers? Four validation tools applied to eight atomic
resolution structures [REF]
 
  659 PRO  ( 768-) B  -   0.16 LOW
 1178 PRO  (1287-) B  -   0.00 LOW
 2203 PRO  ( 768-) D  -   0.16 LOW
 2722 PRO  (1287-) D  -   0.00 LOW
 
# 76 # Warning: Unusual PRO puckering phases
The proline residues listed in the table below have a puckering phase that is
not expected to occur in protein structures. Puckering parameters were
calculated by the method of Cremer and Pople [REF]. Normal PRO rings
approximately show a so-called envelope conformation with the C-gamma atom
above the plane of the ring (phi=+72 degrees), or a half-chair conformation
with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees).
If phi deviates strongly from these values, this is indicative of a very
strange conformation for a PRO residue, and definitely requires a manual
check of the data. Be aware that this is a warning with a low confidence
level. See: Who checks the checkers? Four validation tools applied to eight
atomic resolution structures [REF].
 
   32 PRO  (  54-) A  -   31.8 envelop C-delta (36 degrees)
   41 PRO  (  63-) A  -   10.9 half-chair N/C-delta (18 degrees)
  119 PRO  ( 141-) A  -   99.4 envelop C-beta (108 degrees)
  168 PRO  ( 190-) A  -   32.3 envelop C-delta (36 degrees)
  192 PRO  ( 214-) A  -   47.0 half-chair C-delta/C-gamma (54 degrees)
  325 PRO  ( 347-) A  -   53.0 half-chair C-delta/C-gamma (54 degrees)
  330 PRO  ( 352-) A  -   35.3 envelop C-delta (36 degrees)
  344 PRO  ( 366-) A  -  106.4 envelop C-beta (108 degrees)
  361 PRO  ( 383-) A  -   38.9 envelop C-delta (36 degrees)
  496 PRO  ( 518-) A  -   11.2 half-chair N/C-delta (18 degrees)
  505 PRO  ( 527-) A  -  -59.7 half-chair C-beta/C-alpha (-54 degrees)
  641 PRO  ( 663-) A  -   52.5 half-chair C-delta/C-gamma (54 degrees)
  727 PRO  ( 836-) B  -   32.2 envelop C-delta (36 degrees)
  761 PRO  ( 870-) B  -  100.7 envelop C-beta (108 degrees)
  788 PRO  ( 897-) B  -    8.7 envelop N (0 degrees)
And so on for a total of    50 lines.
 
# 77 # Warning: Backbone oxygen evaluation
The residues listed in the table below have an unusual backbone oxygen
position.
 
For each of the residues in the structure, a search was performed to find
5-residue stretches in the WHAT CHECK database with superposable C-alpha
coordinates, and some restraints on the neighbouring backbone oxygens.
 
In the following table the RMS distance between the backbone oxygen positions
of these matching structures in the database and the position of the backbone
oxygen atom in the current residue is given. If this number is larger than
1.5 a significant number of structures in the database show an alternative
position for the backbone oxygen. If the number is larger than 2.0 most
matching backbone fragments in the database have the peptide plane flipped.
A manual check needs to be performed to assess whether the experimental data
can support that alternative as well. The number in the last column is the
number of database hits (maximum 80) used in the calculation. It is "normal"
that some glycine residues show up in this list, but they are still worth
checking!
 
 2849 GLY  (1424-) D  -  3.10   11
  875 GLY  ( 984-) B  -  1.78   78
 3360 GLY  ( 179-) F  -  1.77   56
 3085 GLY  (1660-) D  -  1.67   42
 1541 GLY  (1660-) B  -  1.60   43
 2200 SER  ( 765-) D  -  1.58   10
 1220 GLY  (1329-) B  -  1.57   50
 3331 LYS  ( 150-) F  -  1.56   48
  702 ASP  ( 811-) B  -  1.55   18
 3171 GLY  ( 179-) E  -  1.55   69
 2246 ASP  ( 811-) D  -  1.53   16
 2764 GLY  (1329-) D  -  1.51   50
 3142 LYS  ( 150-) E  -  1.51   51
 
# 78 # Warning: Possible peptide flips
For the residues listed in the table below, the backbone formed by the
residue mentioned and the one N-terminal of it show systematic deviations
from normality that are consistent with a peptide flip. This can either
be a 180 degree flip of the entire peptide plane or a trans to cis flip.
(Cis to trans flips cannot be detected yet). The type can be TT+, TC-,
or TC+:
TT+ indicates a 180 degree flip of the entire peptide plane.
TC- indicates a trans to cis conversion that requires a flip of the N atom.
TC+ indicates a trans to cis conversion that requires a flip of the O atom.
Note that the method will only work correctly for PDB files with full
isotropic B-factors.
 
 1049 CYS  (1158-) B  - TT+   Highly likely
 2292 ASN  ( 857-) D  - TT+   Highly likely
  209 SER  ( 231-) A  - TT+   Likely
  408 GLU  ( 430-) A  - TT+   Likely
  519 SER  ( 541-) A  - TT+   Likely
  663 LEU  ( 772-) B  - TT+   Likely
  733 ASN  ( 842-) B  - TT+   Likely
  748 ASN  ( 857-) B  - TT+   Likely
  841 GLU  ( 950-) B  - TT+   Likely
  864 ASP  ( 973-) B  - TT+   Likely
 1028 ASN  (1137-) B  - TT+   Likely
 1070 ASN  (1179-) B  - TT+   Likely
 1107 ASP  (1216-) B  - TT+   Likely
 1316 ASP  (1435-) B  - TT+   Likely
 1380 ASP  (1499-) B  - TT+   Likely
And so on for a total of    36 lines.
 
# 79 # Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually short
distance; each bump is listed in only one direction,
 
The contact distances of all atom pairs have been checked. Two atoms are
said to `bump' if they are closer than the sum of their Van der Waals radii
minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom
is used. The first number in the table tells you how much shorter that
specific contact is than the acceptable limit. The second distance is the
distance between the centres of the two atoms.
 
The last text-item on each line represents the status of the atom pair. The
text `INTRA' means that the bump is between atoms that are explicitly listed
in the PDB file. `INTER' means it is an inter-symmetry bump. If the final
column contains the text 'HB', the bump criterion was relaxed because there
could be a hydrogen bond. Similarly relaxed criteria are used for 1--3 and
1--4 interactions (listed as 'B2' and 'B3', respectively). If the last column
is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes
the appearance of the bump somewhat less severe because the atoms probably
are not there anyway. BL, on the other hand, indicates that the bumping atoms
both have a low B-factor, and that makes the bumps more worrisome.
 
It seems likely that at least some of the reported bumps are caused by
administrative errors in the chain names. I.e. covalently bound atoms with
different non-blank chain-names are reported as bumps. In rare cases this is
not an error.
 
Bumps between atoms for which the sum of their occupancies is lower than one
are not reported. If the MODEL number does not exist (as is the case in most
X-ray files), a minus sign is printed instead.
 
  906 MET  (1015-) B  -    SD   <-->    947 GLN  (1056-) B  -    NE2  0.89    2.41  INTRA BF
 2030 ARG  ( 508-) C  -    NH1  <-->   2034 GLN  ( 512-) C  -    O    0.89    1.81  INTRA BF
 2563 GLU  (1128-) D  -    OE1  <-->   2702 GLY  (1267-) D  -    CA   0.75    2.05  INTRA BF
 2587 GLN  (1152-) D  -    NE2  <-->   2633 GLN  (1198-) D  -    OE1  0.73    1.97  INTRA BF
 1398 ASN  (1517-) B  -    ND2  <-->   1402 GLN  (1521-) B  -    OE1  0.64    2.06  INTRA BF
    3 MET  (  25-) A  -    SD   <-->    630 GLN  ( 652-) A  -    NE2  0.60    2.70  INTRA BF
 1002 LYS  (1111-) B  -    CE   <-->   1010 GLN  (1119-) B  -    O    0.57    2.23  INTRA BF
 3096 LEU  ( 104-) E  -    O    <-->   3122 ARG  ( 130-) E  -    NH1  0.57    2.13  INTRA BF
 2536 CYS  (1101-) D  -    SG   <-->   2596 GLN  (1161-) D  -    NE2  0.56    2.74  INTRA BF
  159 SER  ( 181-) A  -    CB   <-->   3238 ARG  ( 246-) E  -    NH2  0.51    2.59  INTRA BF
 1670 ARG  ( 148-) C  -    CZ   <-->   2116 VAL  ( 594-) C  -    CG2  0.50    2.70  INTRA BF
 2192 ALA  ( 757-) D  -    O    <-->   2348 LYS  ( 913-) D  -    NZ   0.49    2.21  INTRA BF
 1062 LYS  (1171-) B  -    O    <-->   1065 ASP  (1174-) B  -    OD1  0.48    1.92  INTRA BF
  881 MET  ( 990-) B  -    O    <-->   1173 TYR  (1282-) B  -    OH   0.48    1.92  INTRA BF
 2030 ARG  ( 508-) C  -    NH1  <-->   2034 GLN  ( 512-) C  -    C    0.47    2.63  INTRA BF
And so on for a total of   585 lines.
 
# 80 # Note: Some notes regarding these bumps
The bumps have been binned in 5 categories ranging from 'please look at'
till 'must fix'. Additionally, the integrated sum of all bumps, the squared
sum of all bumps, and these latter two values normalized by the number of
contacts are listed too for comparison purposes between, for example, small
and large proteins.
 
Total bump value: 76.384
Total bump value per residue: 0.169
Total number of bumps: 585
Total squared bump value: 19.540
Total number of bumps in the mildest bin: 500
Total number of bumps in the second bin: 75
Total number of bumps in the middle bin: 7
Total number of bumps in the fourth bin: 3
Total number of bumps in the worst bin: 0
 
# 81 # Note: Inside/outside distribution check
The following list contains per-residue Z-scores describing how well the
residue's observed accessibility fits the expected one. A positive Z-score
indicates "more exposure than usual", whereas a negative Z-score means
"more buried than usual". The absolute value of the Z-score must be used to
judge the quality. Today WHAT CHECK saw no reason to complain.
 
# 82 # Note: Inside/Outside residue distribution normal
The distribution of residue types over the inside and the outside of the
protein is normal.
 
inside/outside RMS Z-score : 1.013
 
# 83 # Note: Inside/Outside RMS Z-score plot
The Inside/Outside distribution normality RMS Z-score over a 15 residue
window is plotted as function of the residue number. High areas in the plot
(above 1.5) indicate unusual inside/outside patterns.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 84 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 85 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 86 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 87 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 88 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 89 # Warning: Abnormal packing environment for some residues
The residues listed in the table below have an unusual packing environment.
 
The packing environment of the residues is compared with the average packing
environment for all residues of the same type in good PDB files. A low
packing score can indicate one of several things: Poor packing, misthreading
of the sequence through the density, crystal contacts, contacts with a
co-factor, or the residue is part of the active site. It is not uncommon to
see a few of these, but in any case this requires further inspection of the
residue.
 
 2701 TYR  (1266-) D  -  -8.07
 1157 TYR  (1266-) B  -  -7.87
   28 GLN  (  50-) A  -  -7.23
 3162 ARG  ( 170-) E  -  -7.19
 3351 ARG  ( 170-) F  -  -7.19
  395 GLN  ( 417-) A  -  -7.12
 1939 GLN  ( 417-) C  -  -7.10
 1834 GLN  ( 312-) C  -  -7.10
 2386 ARG  ( 951-) D  -  -7.07
 1572 GLN  (  50-) C  -  -7.04
 3426 TYR  ( 245-) F  -  -7.03
  290 GLN  ( 312-) A  -  -7.01
  842 ARG  ( 951-) B  -  -6.96
 3237 TYR  ( 245-) E  -  -6.81
 1435 LEU  (1554-) B  -  -6.77
And so on for a total of    98 lines.
 
# 90 # Warning: Abnormal packing environment for sequential residues
A stretch of at least three sequential residues with a questionable packing
environment was found. This could indicate that these residues are part
of a strange loop. It might also be an indication of misthreading in the
density. However, it can also indicate that one or more residues in this
stretch have other problems such as, for example, missing atoms, very
weird angles or bond lengths, etc.
 
The table below lists the first and last residue in each stretch found,
as well as the average residue score of the series.
 
  960 PHE  (1069-) B  -      963 --- ARG  1072- (B ) -       -4.53
 2505 VAL  (1070-) D  -     2507 --- ARG  1072- (D ) -       -4.79
 3232 ARG  ( 240-) E  -     3234 --- HIS   242- (E ) -       -4.54
 3411 GLN  ( 230-) F  -     3413 --- ASP   232- (F ) -       -4.59
 
# 91 # Note: Structural average packing environment OK
The structural average packing score is within normal ranges.
 
 
Average for range     1 - 3466 :  -0.936
 
# 92 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 93 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 94 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 95 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 96 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 97 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 98 # Warning: Low packing Z-score for some residues
The residues listed in the table below have an unusual packing
environment according to the 2nd generation packing check. The score
listed in the table is a packing normality Z-score: positive means
better than average, negative means worse than average. Only residues
scoring less than -2.50 are listed here. These are the unusual
residues in the structure, so it will be interesting to take a
special look at them.
 
 1181 GLN  (1290-) B  -  -3.35
 2424 GLN  ( 989-) D  -  -3.04
 2371 ILE  ( 936-) D  -  -3.04
 3252 ILE  ( 260-) E  -  -2.94
  515 LEU  ( 537-) A  -  -2.89
  827 ILE  ( 936-) B  -  -2.86
 2790 GLN  (1355-) D  -  -2.77
 1246 GLN  (1355-) B  -  -2.74
 2788 LYS  (1353-) D  -  -2.73
 1617 GLU  (  95-) C  -  -2.71
 1179 ASP  (1288-) B  -  -2.71
 1589 LEU  (  67-) C  -  -2.69
 2059 LEU  ( 537-) C  -  -2.68
 2724 HIS  (1289-) D  -  -2.68
 2722 PRO  (1287-) D  -  -2.67
 3348 GLY  ( 167-) F  -  -2.66
  725 ARG  ( 834-) B  -  -2.62
 1178 PRO  (1287-) B  -  -2.61
 2908 TYR  (1483-) D  -  -2.59
 1244 LYS  (1353-) B  -  -2.58
  271 ILE  ( 293-) A  -  -2.54
 2425 MET  ( 990-) D  -  -2.54
 1835 ASN  ( 313-) C  -  -2.52
 2269 ARG  ( 834-) D  -  -2.51
 1245 ASP  (1354-) B  -  -2.51
 
# 99 # Warning: Abnormal packing Z-score for sequential residues
A stretch of at least four sequential residues with a 2nd generation packing
Z-score below -1.75 was found. This could indicate that these residues are
part of a strange loop or that the residues in this range are incomplete,
but it might also be an indication of misthreading.
 
The table below lists the first and last residue in each stretch found,
as well as the average residue Z-score of the series.
 
 1177 ALA  (1286-) B  -   ---  1182 GLU  (1291-) B  -      -2.38
 1243 ALA  (1352-) B  -   ---  1246 GLN  (1355-) B  -      -2.23
 1614 ALA  (  92-) C  -   ---  1617 GLU  (  95-) C  -      -1.79
 2422 VAL  ( 987-) D  -   ---  2425 MET  ( 990-) D  -      -2.02
 2721 ALA  (1286-) D  -   ---  2725 GLN  (1290-) D  -      -2.13
 2787 ALA  (1352-) D  -   ---  2790 GLN  (1355-) D  -      -2.09
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 100 # Note: Second generation quality Z-score plot
The second generation quality Z-score smoothed over a 10 residue window
is plotted as function of the residue number. Low areas in the plot (below
-1.3) indicate unusual packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 101 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 102 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 103 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 104 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 105 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 106 # Warning: No crystallisation information
No, or very inadequate, crystallisation information was observed upon
reading the PDB file header records. This information should be available
in the form of a series of REMARK 280 lines. Without this information a
few things, such as checking ions in the structure, cannot be performed
optimally.
 
# 107 # Error: His, Asn, Gln side chain flips
Listed here are Histidine, Asparagine or Glutamine residues for
which the orientation determined from hydrogen bonding analysis are
different from the assignment given in the input. Either they could
form energetically more favourable hydrogen bonds if the terminal
group was rotated by 180 degrees, or there is no assignment in the
input file (atom type 'A') but an assignment could be made. Be aware,
though, that if the topology could not be determined for one or more
ligands, then this option will make errors.
 
  111 GLN  ( 133-) A  -
  132 HIS  ( 154-) A  -
  318 GLN  ( 340-) A  -
  431 ASN  ( 453-) A  -
  557 GLN  ( 579-) A  -
  630 GLN  ( 652-) A  -
  639 GLN  ( 661-) A  -
  651 ASN  ( 760-) B  -
  759 HIS  ( 868-) B  -
  830 ASN  ( 939-) B  -
  934 GLN  (1043-) B  -
  946 GLN  (1055-) B  -
 1017 HIS  (1126-) B  -
 1027 ASN  (1136-) B  -
 1070 ASN  (1179-) B  -
And so on for a total of    43 lines.
 
# 108 # Note: Histidine type assignments
For all complete HIS residues in the structure a tentative assignment to
HIS-D (protonated on ND1), HIS-E (protonated on NE2), or HIS-H (protonated
on both ND1 and NE2, positively charged) is made based on the hydrogen bond
network. A second assignment is made based on which of the Engh and Huber
[REF] histidine geometries fits best to the structure.
 
In the table below all normal histidine residues are listed. The assignment
based on the geometry of the residue is listed first, together with the RMS
Z-score for the fit to the Engh and Huber parameters. For all residues where
the H-bond assignment is different, the assignment is listed in the last
columns, together with its RMS Z-score to the Engh and Huber parameters.
 
As always, the RMS Z-scores should be close to 1.0 if the residues were
restrained to the Engh and Huber parameters during refinement, and if
enough (high resolution) data is available.
 
Please note that because the differences between the geometries of the
different types are small it is possible that the geometric assignment given
here does not correspond to the type used in refinement. This is especially
true if the RMS Z-scores are much higher than 1.0.
 
If the two assignments differ, or the `geometry' RMS Z-score is high, it is
advisable to verify the hydrogen bond assignment, check the HIS type used
during the refinement and possibly adjust it.
 
   25 HIS  (  47-) A  -   HIS-E   0.56 HIS-H   0.71
   38 HIS  (  60-) A  -   HIS-E   0.37 HIS-D   0.83
   60 HIS  (  82-) A  -   HIS-E   0.68
  132 HIS  ( 154-) A  -   HIS-E   0.53
  311 HIS  ( 333-) A  -   HIS-E   0.51 HIS-D   0.96
  334 HIS  ( 356-) A  -   HIS-E   0.46 HIS-D   0.87
  392 HIS  ( 414-) A  -   HIS-E   0.70
  435 HIS  ( 457-) A  -   HIS-E   0.57
  461 HIS  ( 483-) A  -   HIS-H   0.44 HIS-D   0.62
  567 HIS  ( 589-) A  -   HIS-E   0.52 HIS-D   0.74
  759 HIS  ( 868-) B  -   HIS-E   0.43 HIS-D   0.73
  773 HIS  ( 882-) B  -   HIS-E   0.45
  809 HIS  ( 918-) B  -   HIS-E   0.60 HIS-D   1.05
  810 HIS  ( 919-) B  -   HIS-E   0.65 HIS-D   1.03
  893 HIS  (1002-) B  -   HIS-E   0.47
And so on for a total of    54 lines.
 
# 109 # Warning: Buried unsatisfied hydrogen bond donors
The buried hydrogen bond donors listed in the table below have a hydrogen
atom that is not involved in a hydrogen bond in the optimized hydrogen bond
network.
 
Hydrogen bond donors that are buried inside the protein normally use all of
their hydrogens to form hydrogen bonds within the protein. If there are any
non hydrogen bonded buried hydrogen bond donors in the structure they will
be listed here. In very good structures the number of listed atoms will tend
to zero.
 
Waters are not listed by this option.
 
   11 ILE  (  33-) A  -    N
   16 SER  (  38-) A  -    N
   39 ASP  (  61-) A  -    N
   45 LEU  (  67-) A  -    N
   46 VAL  (  68-) A  -    N
   68 ILE  (  90-) A  -    N
   75 LYS  (  97-) A  -    N
   83 PHE  ( 105-) A  -    N
  106 GLY  ( 128-) A  -    N
  108 LEU  ( 130-) A  -    N
  116 ILE  ( 138-) A  -    N
  120 GLY  ( 142-) A  -    N
  133 LYS  ( 155-) A  -    N
  149 GLU  ( 171-) A  -    N
  159 SER  ( 181-) A  -    N
And so on for a total of   395 lines.
 
# 110 # Warning: Buried unsatisfied hydrogen bond acceptors
The buried side-chain hydrogen bond acceptors listed in the table below are
not involved in a hydrogen bond in the optimized hydrogen bond network.
 
Side-chain hydrogen bond acceptors buried inside the protein normally form
hydrogen bonds within the protein. If there are any not hydrogen bonded in
the optimized hydrogen bond network they will be listed here.
 
Waters are not listed by this option.
 
   10 ASN  (  32-) A  -    OD1
   18 GLU  (  40-) A  -    OE1
   50 GLU  (  72-) A  -    OE1
   60 HIS  (  82-) A  -    ND1
  264 GLU  ( 286-) A  -    OE2
  474 ASN  ( 496-) A  -    OD1
  630 GLN  ( 652-) A  -    OE1
  735 GLN  ( 844-) B  -    OE1
  737 GLU  ( 846-) B  -    OE2
  839 ASP  ( 948-) B  -    OD1
  917 HIS  (1026-) B  -    ND1
  946 GLN  (1055-) B  -    OE1
 1003 GLN  (1112-) B  -    OE1
 1043 GLN  (1152-) B  -    OE1
 1068 GLU  (1177-) B  -    OE1
And so on for a total of    47 lines.
 
# 111 # Note: Some notes regarding these donors and acceptors
The donors and acceptors have been counted, also as function of their
accessibility. The buried donors and acceptors have been binned in five
categories ranging from not forming any hydrogen bond till forming a poor
till perfect hydrogen bond. Obviously, the buried donors and acceptors
with no or just a poor hydrogen bond should be a topic of concern. As every
protein contains more acceptors than donors, unsatisfied donors are more in
need of attention than unsatisfied acceptors.
 
Total number of donors: 4947
- of which buried: 2352
Total number of acceptors: 5418
- of which buried: 1960
Total number of donor+acceptors: 587
  (e.g. the Ser Ogamma that can donate and accept)
- of which buried: 155
Buried donors: 2352
- without H-bond: 367
- essentially without H-bond: 1
- with only a very poor H-bond: 23
- with a poor H-bond: 51
- with a H-bond: 1910
Buried acceptors: 1960
- without H-bond: 407
- essentially without H-bond: 1
- with only a very poor H-bond: 19
- with a poor H-bond: 58
- with a H-bond: 1475
 
# 112 # Note: Content of the PDB file as interpreted by WHAT CHECK
Content of the PDB file as interpreted by WHAT CHECK.
WHAT CHECK has read your PDB file, and stored it internally in what is called
'the soup'. The content of this soup is listed here. An extensive explanation
of all frequently used WHAT CHECK output formats can be found at
swift.cmbi.ru.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
 
     1     1 (   23)   642 (  664) A Protein             /zata/tempdir/5fo...
     2   643 (  752)  1262 ( 1371) B Protein             /zata/tempdir/5fo...
     3  1263 ( 1382)  1544 ( 1663) B Protein             /zata/tempdir/5fo...
     4  1545 (   23)  2186 (  664) C Protein             /zata/tempdir/5fo...
     5  2187 (  752)  2806 ( 1371) D Protein             /zata/tempdir/5fo...
     6  2807 ( 1382)  3088 ( 1663) D Protein             /zata/tempdir/5fo...
     7  3089 (   97)  3277 (  285) E Protein             /zata/tempdir/5fo...
     8  3278 (   97)  3466 (  285) F Protein             /zata/tempdir/5fo...
     9  3467 ( 1663)  3467 ( 1663) B N O2 <-  1544       /zata/tempdir/5fo...
    10  3468 ( 1663)  3468 ( 1663) D N O2 <-  3088       /zata/tempdir/5fo...
 
# 113 # Note: Summary report
This is an overall summary of the quality of the structure as compared with
current reliable structures. Numbers in brackets are the average and standard
deviation observed for a large number of files determined with a similar
resolution.
 
The second table mostly gives an impression of how well the model conforms
to common refinement restraint values. These numbers are less than 1.0 if the
spread in data is too little, and larger than 1.0 when the spread is too
large. The former does not need to be a problem, the latter always is bad.
 
 Structure Z-scores, positive is better than average:
  Resolution read from PDB file  :   4.190
  1st generation packing quality :  -1.090
  2nd generation packing quality :  -2.846
  Ramachandran plot appearance   :  -4.409 (bad)
  chi-1/chi-2 rotamer normality  :  -5.884 (bad)
  Backbone conformation          :  -0.833
  Inside/Outside distribution    :   1.013
 
 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.456 (tight)
  Bond angles                    :   0.745
  Omega angle restraints         :   1.173
  Side chain planarity           :   0.842
  Improper dihedral distribution :   0.597
  B-factor distribution          :   0.365
 
# 114 # Note: Introduction to refinement recommendations
First, be aware that the recommendations for crystallographers listed below
are produced by a computer program that was written by a guy who got his
PhD in NMR...
 
We have tried to convert the messages written in this report into a small
set of things you can do with your refinement software to get a better
structure. The things you should do first are listed first. And in some
cases you should first fix that problem, then refine a bit further, and
then run WHAT CHECK again before looking at other problems. If, for example,
WHAT CHECK has found a problem with the SCALE and CRYST cards, then you must
first fix that problem, refine the structure a bit further, and run WHAT
CHECK again because errors in the SCALE and or CRYST card can lead to many
problems elsewhere in the validation process.
 
It is also important to keep in mind that WHAT CHECK is software and that it
occasionally totally misunderstands what is the cause of a problem. But, if
WHAT CHECK lists a problem there normally is a problem albeit that it not
always is the actual problem that gets listed.
 
# 115 # Note: No crippling problems detected
Some problems can be so crippling that they negatively influence the
validity of other validation steps. If such a problem is detected, it must
be solved and some further refinemnet must be done before you can continue
working with a new WHAT CHECK report. In this file such problems were not
detected. You can therefore try to fix as many problems in one go as you
want.
 
# 116 # Error: Bumps in your structure
Upon analysing the bumps in your structure, WHAT CHECK got very, very
worried. Sometimes this means that you have forgotten to lower the
occupancy of overlapping ligands, residues, or water molecules. But,
whatever is the origin of this problem, you have to analyse it and
fix it.
 
# 117 # Note: Bond angle variabilty Z-score high
With a resolution of 3 Angstrom or worse, you dont have enough data to
warrant the bond angle variability that we observed. So, tighten the screws
on the bond angle target values.
 
# 118 # Note: His, Asn, Gln side chain flips.
His, Asn, and Gln have an asymmetry in their side chain that is hard to
detect unless you have data at much better than 1.0 Angstrom resolution.
WHAT CHECK thinks that your structure contains His, Asn, or Gln residues that
will make better hydrogen bonds when flipped around their chi-2, chi-2, or
chi-3 side chain torsion angle, respectively. You better
check these Asn, His, and Gln residues, and if you use a refinement program
that includes molecular dynamics, then you must (after the
flips were made) refine a bit further before running WHAT CHECK again.
 
# 119 # Warning: Troublesome residues
The residues listed in the table below need to be inspected
 
This table is a very rough attempt to sort the residues according to how
badly they need your attention. The idea is that when you sit in  in front
of the graphics screen and study the residues with the electron density
present that you improve the structure most by dealing with the top residues
in this list first.
 
  642 GLN  ( 664-) A  -     16.32
 2701 TYR  (1266-) D  -     16.14
 2186 GLN  ( 664-) C  -     16.08
 1572 GLN  (  50-) C  -     16.07
 1157 TYR  (1266-) B  -     15.74
  842 ARG  ( 951-) B  -     15.06
 2791 LEU  (1356-) D  -     14.81
  639 GLN  ( 661-) A  -     14.48
 1402 GLN  (1521-) B  -     14.48
   28 GLN  (  50-) A  -     14.47
 3162 ARG  ( 170-) E  -     14.41
 3426 TYR  ( 245-) F  -     14.38
 3351 ARG  ( 170-) F  -     14.37
  395 GLN  ( 417-) A  -     14.25
 1939 GLN  ( 417-) C  -     14.20
And so on for a total of   401 lines.
==============
 
 
WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).
 
WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra
    information)
 
PDB facilities
    Touw WG, Baakman C, Black J, te Beek TA, Krieger E, Joosten RP, Vriend G.
      A series of PDB-related databanks for everyday needs.
    Nucleic Acids Research D364-368 Database issue (2015).
 
Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991) and
    R.Engh and R.Huber,
    International Tables for Crystallography (2001)
 
 
Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).
 
DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).
 
Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).
 
Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).
 
Peptide flips
    Touw WG, Joosten RP, Vriend G.
      Detection of trans-cis flips and peptide-plane flips in protein
      structures.
    Acta Crystallogr D Biological Crystallograhy 71, 1604-1614 (2015).
 
Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).
 
Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).
 
Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).
 
Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).
    R.W.W. Hooft, C.Sander and G.Vriend,
      Objectively judging the quality of a protein structure from a
      Ramachandran plot
    CABIOS (1997), 13, 425--430.
 
Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).
 
Tau angle
    W.G.Touw and G.Vriend
      On the complexity of Engh and Huber refinement restraints: the angle
      tau as example.
    Acta Crystallogr D 66, 1341--1350 (2010).
 
Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).
 
    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).
 
    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).
 
Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.
==============
 
 
WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).
 
WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra
    information)
 
PDB facilities
    Touw WG, Baakman C, Black J, te Beek TA, Krieger E, Joosten RP, Vriend G.
      A series of PDB-related databanks for everyday needs.
    Nucleic Acids Research D364-368 Database issue (2015).
 
Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991) and
    R.Engh and R.Huber,
    International Tables for Crystallography (2001)
 
 
Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).
 
DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).
 
Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).
 
Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).
 
Peptide flips
    Touw WG, Joosten RP, Vriend G.
      Detection of trans-cis flips and peptide-plane flips in protein
      structures.
    Acta Crystallogr D Biological Crystallograhy 71, 1604-1614 (2015).
 
Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).
 
Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).
 
Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).
 
Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).
    R.W.W. Hooft, C.Sander and G.Vriend,
      Objectively judging the quality of a protein structure from a
      Ramachandran plot
    CABIOS (1997), 13, 425--430.
 
Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).
 
Tau angle
    W.G.Touw and G.Vriend
      On the complexity of Engh and Huber refinement restraints: the angle
      tau as example.
    Acta Crystallogr D 66, 1341--1350 (2010).
 
Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).
 
    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).
 
    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).
 
Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.
