Starting phenix.real_space_refine
on Fri Dec  8 00:28:05 2023 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xum_33474/12_2023/7xum_33474.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xum_33474/12_2023/7xum_33474.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xum_33474/12_2023/7xum_33474.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xum_33474/12_2023/7xum_33474.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xum_33474/12_2023/7xum_33474.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xum_33474/12_2023/7xum_33474.pdb"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Cu      1      5.60       5
     S      39      5.16       5
     C    3948      2.51       5
     N    1045      2.21       5
     O    1122      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU 1382": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 6155
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 817, 6155
          Unusual residues: {' CU': 1}
          Classifications: {'peptide': 816, 'undetermined': 1}
          Link IDs: {'PTRANS': 33, 'TRANS': 782, None: 1}
            Not linked:
              pdbres="GLY A1405 "
              pdbres=" CU A2000 "
          Chain breaks: 1
  Time building chain proxies: 3.85, per 1000 atoms: 0.63
  Number of scatterers: 6155
  At special positions: 0
  Unit cell: (142.974, 91.26, 78.078, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cu      1     28.99
     S      39     16.00
     O    1122      8.00
     N    1045      7.00
     C    3948      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.29
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1510

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 6 sheets defined
      53.6% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 577 through 589
      removed outlier: 3.514A  pdb=" N   THR A 589 " --> pdb=" O   LYS A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 626
    Processing helix  chain 'A' and resid 637 through 642
      removed outlier: 4.167A  pdb=" N   LEU A 641 " --> pdb=" O   ASN A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 659
      removed outlier: 3.965A  pdb=" N   VAL A 659 " --> pdb=" O   LEU A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 673
      removed outlier: 3.576A  pdb=" N   ILE A 673 " --> pdb=" O   ILE A 669 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 694 through 711
      removed outlier: 3.565A  pdb=" N   GLY A 711 " --> pdb=" O   GLN A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 723
    Processing helix  chain 'A' and resid 728 through 754
      removed outlier: 4.066A  pdb=" N   LEU A 732 " --> pdb=" O   ASN A 728 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ILE A 733 " --> pdb=" O   MET A 729 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   SER A 744 " --> pdb=" O   ALA A 740 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 765 through 787
      removed outlier: 3.640A  pdb=" N   MET A 769 " --> pdb=" O   ASP A 765 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL A 772 " --> pdb=" O   PRO A 768 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   PHE A 773 " --> pdb=" O   MET A 769 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   HIS A 782 " --> pdb=" O   ARG A 778 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   LYS A 787 " --> pdb=" O   LEU A 783 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 797
    Processing helix  chain 'A' and resid 894 through 907
      removed outlier: 3.973A  pdb=" N   GLN A 907 " --> pdb=" O   VAL A 903 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 922
    Processing helix  chain 'A' and resid 923 through 946
      removed outlier: 3.811A  pdb=" N   PHE A 927 " --> pdb=" O   TYR A 923 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 952
      removed outlier: 4.440A  pdb=" N   VAL A 950 " --> pdb=" O   ASP A 946 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 962 through 978
      removed outlier: 3.565A  pdb=" N   VAL A 966 " --> pdb=" O   SER A 962 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ILE A 967 " --> pdb=" O   GLN A 963 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL A 978 " --> pdb=" O   THR A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 989
      removed outlier: 3.866A  pdb=" N   LEU A 987 " --> pdb=" O   SER A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 989 through 1004
      removed outlier: 3.853A  pdb=" N   THR A 993 " --> pdb=" O   LEU A 989 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ALA A 994 " --> pdb=" O   ALA A 990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1012 through 1018
      removed outlier: 3.997A  pdb=" N   GLU A1016 " --> pdb=" O   GLY A1012 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1052 through 1065
    Processing helix  chain 'A' and resid 1069 through 1084
      removed outlier: 3.587A  pdb=" N   ALA A1074 " --> pdb=" O   PRO A1070 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1114
      removed outlier: 3.547A  pdb=" N   LEU A1113 " --> pdb=" O   VAL A1109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1150 through 1157
      removed outlier: 3.723A  pdb=" N   LEU A1154 " --> pdb=" O   ASN A1150 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG A1155 " --> pdb=" O   ARG A1151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1162 through 1167
    Processing helix  chain 'A' and resid 1168 through 1175
      removed outlier: 4.368A  pdb=" N   HIS A1172 " --> pdb=" O   ALA A1168 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LYS A1175 " --> pdb=" O   ASP A1171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1201 through 1213
      removed outlier: 4.094A  pdb=" N   VAL A1206 " --> pdb=" O   ALA A1202 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   HIS A1207 " --> pdb=" O   ALA A1203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1223 through 1235
      removed outlier: 3.595A  pdb=" N   ALA A1227 " --> pdb=" O   ASN A1223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1249 through 1257
    Processing helix  chain 'A' and resid 1268 through 1270
      No H-bonds generated for 'chain 'A' and resid 1268 through 1270'
    Processing helix  chain 'A' and resid 1271 through 1278
      removed outlier: 3.531A  pdb=" N   GLN A1277 " --> pdb=" O   PRO A1273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1304 through 1340
      removed outlier: 4.230A  pdb=" N   VAL A1308 " --> pdb=" O   LEU A1304 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   ARG A1320 " --> pdb=" O   ARG A1316 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ILE A1321 " --> pdb=" O   THR A1317 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ARG A1322 " --> pdb=" O   VAL A1318 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   TYR A1331 " --> pdb=" O   LEU A1327 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   ASN A1332 " --> pdb=" O   ALA A1328 " (cutoff:3.500A)
      Proline residue:  A1337  - end of helix
    Processing helix  chain 'A' and resid 1351 through 1372
      removed outlier: 3.552A  pdb=" N   SER A1356 " --> pdb=" O   PRO A1352 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ALA A1358 " --> pdb=" O   MET A1354 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   MET A1359 " --> pdb=" O   GLY A1355 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ALA A1361 " --> pdb=" O   ALA A1357 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   SER A1362 " --> pdb=" O   ALA A1358 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL A1364 " --> pdb=" O   ALA A1360 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER A1365 " --> pdb=" O   ALA A1361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1373 through 1375
      No H-bonds generated for 'chain 'A' and resid 1373 through 1375'
    Processing helix  chain 'A' and resid 1380 through 1389
      removed outlier: 3.961A  pdb=" N   GLN A1387 " --> pdb=" O   ARG A1383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1396 through 1400
    Processing sheet with id=AA1, first strand: chain 'A' and resid 592 through 598
      removed outlier: 4.648A  pdb=" N   TYR A 594 " --> pdb=" O   LYS A 607 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LYS A 607 " --> pdb=" O   TYR A 594 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LYS A 603 " --> pdb=" O   ALA A 598 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   HIS A 628 " --> pdb=" O   THR A 571 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 687 through 689
      removed outlier: 3.884A  pdb=" N   ILE A 689 " --> pdb=" O   LEU A 692 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 814 through 821
      removed outlier: 4.899A  pdb=" N   ARG A 816 " --> pdb=" O   THR A 807 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   THR A 807 " --> pdb=" O   ARG A 816 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   THR A 804 " --> pdb=" O   LYS A 832 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ILE A 830 " --> pdb=" O   VAL A 806 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   LEU A 884 " --> pdb=" O   LEU A 846 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   GLY A 843 " --> pdb=" O   VAL A 872 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 864 through 866
      removed outlier: 3.937A  pdb=" N   ASP A 853 " --> pdb=" O   ILE A 877 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ILE A 877 " --> pdb=" O   ASP A 853 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1007 through 1009
      removed outlier: 3.758A  pdb=" N   VAL A1298 " --> pdb=" O   LEU A1008 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   VAL A1262 " --> pdb=" O   MET A1280 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   VAL A1282 " --> pdb=" O   VAL A1262 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   MET A1264 " --> pdb=" O   VAL A1282 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   THR A1023 " --> pdb=" O   ALA A1263 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   VAL A1265 " --> pdb=" O   THR A1023 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   MET A1025 " --> pdb=" O   VAL A1265 " (cutoff:3.500A)
      removed outlier: 8.800A  pdb=" N   PHE A1240 " --> pdb=" O   VAL A1216 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   LEU A1218 " --> pdb=" O   PHE A1240 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1038 through 1044
      removed outlier: 7.224A  pdb=" N   ALA A1193 " --> pdb=" O   MET A1040 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   VAL A1042 " --> pdb=" O   MET A1191 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   MET A1191 " --> pdb=" O   VAL A1042 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   LEU A1044 " --> pdb=" O   CYS A1189 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   CYS A1189 " --> pdb=" O   LEU A1044 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   LEU A1188 " --> pdb=" O   ILE A1184 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ILE A1184 " --> pdb=" O   LEU A1188 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLY A1190 " --> pdb=" O   VAL A1182 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL A1182 " --> pdb=" O   GLY A1190 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU A1181 " --> pdb=" O   GLY A1149 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   GLY A1149 " --> pdb=" O   LEU A1181 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   LYS A1105 " --> pdb=" O   ASP A1093 " (cutoff:3.500A)
      removed outlier: 5.015A  pdb=" N   ASP A1093 " --> pdb=" O   LYS A1105 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   SER A1107 " --> pdb=" O   CYS A1091 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   CYS A1091 " --> pdb=" O   SER A1107 " (cutoff:3.500A)

    308 hydrogen bonds defined for protein.
    897 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.12

  Time building geometry restraints manager: 2.50 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.35: 1997
        1.35 -     1.46: 1282
        1.46 -     1.58: 2914
        1.58 -     1.70: 0
        1.70 -     1.82: 67
  Bond restraints: 6260
  Sorted by residual:
  bond pdb=" CG1 ILE A1021 "
       pdb=" CD1 ILE A1021 "
    ideal  model  delta    sigma   weight residual
    1.513  1.462  0.051 3.90e-02 6.57e+02 1.69e+00
  bond pdb=" CB  ASP A1267 "
       pdb=" CG  ASP A1267 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.51e-01
  bond pdb=" C   ASN A 635 "
       pdb=" N   PRO A 636 "
    ideal  model  delta    sigma   weight residual
    1.334  1.353 -0.019 2.34e-02 1.83e+03 6.77e-01
  bond pdb=" CB  MET A1040 "
       pdb=" CG  MET A1040 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 5.97e-01
  bond pdb=" C   MET A1344 "
       pdb=" N   PRO A1345 "
    ideal  model  delta    sigma   weight residual
    1.334  1.345 -0.011 1.51e-02 4.39e+03 5.41e-01
  ... (remaining 6255 not shown)

  Histogram of bond angle deviations from ideal:
       99.66 -   106.54: 183
      106.54 -   113.42: 3635
      113.42 -   120.31: 2176
      120.31 -   127.19: 2443
      127.19 -   134.07: 65
  Bond angle restraints: 8502
  Sorted by residual:
  angle pdb=" N   VAL A1334 "
        pdb=" CA  VAL A1334 "
        pdb=" C   VAL A1334 "
      ideal   model   delta    sigma   weight residual
     112.96  108.05    4.91 1.00e+00 1.00e+00 2.41e+01
  angle pdb=" N   VAL A1249 "
        pdb=" CA  VAL A1249 "
        pdb=" C   VAL A1249 "
      ideal   model   delta    sigma   weight residual
     113.71  109.15    4.56 9.50e-01 1.11e+00 2.30e+01
  angle pdb=" N   GLY A 988 "
        pdb=" CA  GLY A 988 "
        pdb=" C   GLY A 988 "
      ideal   model   delta    sigma   weight residual
     112.50  116.47   -3.97 1.16e+00 7.43e-01 1.17e+01
  angle pdb=" CA  MET A 671 "
        pdb=" CB  MET A 671 "
        pdb=" CG  MET A 671 "
      ideal   model   delta    sigma   weight residual
     114.10  120.20   -6.10 2.00e+00 2.50e-01 9.31e+00
  angle pdb=" CA  VAL A1249 "
        pdb=" C   VAL A1249 "
        pdb=" N   ALA A1250 "
      ideal   model   delta    sigma   weight residual
     119.87  116.50    3.37 1.34e+00 5.57e-01 6.34e+00
  ... (remaining 8497 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 3390
       17.29 -    34.59: 322
       34.59 -    51.88: 61
       51.88 -    69.18: 4
       69.18 -    86.47: 5
  Dihedral angle restraints: 3782
    sinusoidal: 1444
      harmonic: 2338
  Sorted by residual:
  dihedral pdb=" CB  GLU A 567 "
           pdb=" CG  GLU A 567 "
           pdb=" CD  GLU A 567 "
           pdb=" OE1 GLU A 567 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   81.63  -81.63     1      3.00e+01 1.11e-03 9.11e+00
  dihedral pdb=" CA  HIS A1247 "
           pdb=" C   HIS A1247 "
           pdb=" N   LYS A1248 "
           pdb=" CA  LYS A1248 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.99   15.01     0      5.00e+00 4.00e-02 9.02e+00
  dihedral pdb=" CB  GLU A1293 "
           pdb=" CG  GLU A1293 "
           pdb=" CD  GLU A1293 "
           pdb=" OE1 GLU A1293 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -80.33   80.33     1      3.00e+01 1.11e-03 8.87e+00
  ... (remaining 3779 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 597
       0.029 -    0.058: 278
       0.058 -    0.087: 94
       0.087 -    0.116: 69
       0.116 -    0.146: 8
  Chirality restraints: 1046
  Sorted by residual:
  chirality pdb=" CA  THR A 766 "
            pdb=" N   THR A 766 "
            pdb=" C   THR A 766 "
            pdb=" CB  THR A 766 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.30e-01
  chirality pdb=" CA  ASP A1267 "
            pdb=" N   ASP A1267 "
            pdb=" C   ASP A1267 "
            pdb=" CB  ASP A1267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.36e-01
  chirality pdb=" CA  ILE A1194 "
            pdb=" N   ILE A1194 "
            pdb=" C   ILE A1194 "
            pdb=" CB  ILE A1194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  ... (remaining 1043 not shown)

  Planarity restraints: 1064
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A1344 "    0.027 5.00e-02 4.00e+02   4.10e-02 2.69e+00
        pdb=" N   PRO A1345 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A1345 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A1345 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 911 "    0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO A 912 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 912 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 912 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 820 "    0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO A 821 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 821 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 821 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1061 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 34
        2.53 -     3.12: 4698
        3.12 -     3.72: 9550
        3.72 -     4.31: 12304
        4.31 -     4.90: 20650
  Nonbonded interactions: 47236
  Sorted by model distance:
  nonbonded pdb=" CD1 ILE A 733 "
            pdb="CU    CU A2000 "
     model   vdw
     1.938 2.660
  nonbonded pdb=" OG1 THR A 804 "
            pdb=" O   LYS A 832 "
     model   vdw
     2.202 2.440
  nonbonded pdb=" OG1 THR A 858 "
            pdb=" OE1 GLU A 860 "
     model   vdw
     2.216 2.440
  nonbonded pdb=" NH2 ARG A1320 "
            pdb=" OE1 GLN A1372 "
     model   vdw
     2.249 2.520
  nonbonded pdb=" OG  SER A1398 "
            pdb=" OE1 GLN A1399 "
     model   vdw
     2.305 2.440
  ... (remaining 47231 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          3.350
  Check model and map are aligned:         0.110
  Set scattering table:                    0.060
  Process input model:                     21.770
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051   6260  Z= 0.153
  Angle     :  0.565   7.359   8502  Z= 0.291
  Chirality :  0.043   0.146   1046
  Planarity :  0.003   0.041   1064
  Dihedral  : 13.816  86.471   2272
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.30), residues: 812
  helix:  0.68 (0.27), residues: 380
  sheet:  0.01 (0.48), residues: 117
  loop : -1.02 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP A 779 
   HIS   0.002   0.000   HIS A 782 
   PHE   0.005   0.001   PHE A 972 
   TYR   0.006   0.001   TYR A 953 
   ARG   0.004   0.000   ARG A 969 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.673 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1721
  time to fit residues: 27.0055
Evaluate side-chains
  99 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.717 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0121
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 24 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 580 HIS
** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6260  Z= 0.236
  Angle     :  0.578   8.527   8502  Z= 0.295
  Chirality :  0.044   0.162   1046
  Planarity :  0.004   0.041   1064
  Dihedral  :  3.722  13.654    854
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 11.83 %
    Favored  : 86.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.30), residues: 812
  helix:  0.70 (0.27), residues: 387
  sheet: -0.08 (0.47), residues: 113
  loop : -1.00 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP A1153 
   HIS   0.004   0.001   HIS A1312 
   PHE   0.006   0.001   PHE A 627 
   TYR   0.008   0.001   TYR A 953 
   ARG   0.002   0.000   ARG A 952 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.747 
Fit side-chains
  outliers start: 11
  outliers final: 9
  residues processed: 116
  average time/residue: 0.1686
  time to fit residues: 26.6638
Evaluate side-chains
  109 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.688 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0881
  time to fit residues: 2.1822
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 50 optimal weight:    8.9990
   chunk 20 optimal weight:    0.4980
   chunk 73 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 59 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.8186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6260  Z= 0.173
  Angle     :  0.528   5.985   8502  Z= 0.267
  Chirality :  0.043   0.151   1046
  Planarity :  0.004   0.040   1064
  Dihedral  :  3.659  14.649    854
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 15.53 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.30), residues: 812
  helix:  0.89 (0.27), residues: 387
  sheet: -0.12 (0.46), residues: 116
  loop : -0.98 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP A1353 
   HIS   0.004   0.001   HIS A1312 
   PHE   0.007   0.001   PHE A 627 
   TYR   0.006   0.001   TYR A 953 
   ARG   0.002   0.000   ARG A 952 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.757 
Fit side-chains
  outliers start: 8
  outliers final: 3
  residues processed: 112
  average time/residue: 0.1591
  time to fit residues: 24.7472
Evaluate side-chains
  103 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.718 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0585
  time to fit residues: 1.3521
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 73 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0970
   chunk 70 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   6260  Z= 0.156
  Angle     :  0.526  10.903   8502  Z= 0.262
  Chirality :  0.043   0.182   1046
  Planarity :  0.004   0.039   1064
  Dihedral  :  3.620  13.589    854
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 17.90 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.30), residues: 812
  helix:  1.00 (0.27), residues: 387
  sheet: -0.03 (0.46), residues: 116
  loop : -1.04 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP A1353 
   HIS   0.001   0.000   HIS A 782 
   PHE   0.006   0.001   PHE A 627 
   TYR   0.006   0.001   TYR A 953 
   ARG   0.001   0.000   ARG A 969 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.646 
Fit side-chains
  outliers start: 9
  outliers final: 6
  residues processed: 106
  average time/residue: 0.1669
  time to fit residues: 24.5106
Evaluate side-chains
  103 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.775 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0602
  time to fit residues: 1.6682
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 58 optimal weight:    0.1980
   chunk 32 optimal weight:    7.9990
   chunk 66 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0670
   chunk 26 optimal weight:    0.0770
   chunk 15 optimal weight:    5.9990
   overall best weight:    1.6680

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 849 ASN
** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1312 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6260  Z= 0.242
  Angle     :  0.569   9.980   8502  Z= 0.284
  Chirality :  0.044   0.150   1046
  Planarity :  0.004   0.038   1064
  Dihedral  :  3.769  12.926    854
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 18.20 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.29), residues: 812
  helix:  0.69 (0.26), residues: 391
  sheet: -0.14 (0.46), residues: 119
  loop : -1.06 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP A1153 
   HIS   0.007   0.001   HIS A1312 
   PHE   0.007   0.001   PHE A 773 
   TYR   0.009   0.001   TYR A 953 
   ARG   0.003   0.000   ARG A1320 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.694 
Fit side-chains
  outliers start: 12
  outliers final: 7
  residues processed: 106
  average time/residue: 0.1537
  time to fit residues: 22.5571
Evaluate side-chains
  104 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.754 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0630
  time to fit residues: 1.8041
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 45 optimal weight:    0.0980
   chunk 19 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9990
   chunk 65 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 25 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9980
   chunk 75 optimal weight:    0.0470
   chunk 8 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0980
   overall best weight:    0.4078

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.056   6260  Z= 0.151
  Angle     :  0.529   6.703   8502  Z= 0.261
  Chirality :  0.042   0.145   1046
  Planarity :  0.003   0.043   1064
  Dihedral  :  3.627  14.478    854
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 18.79 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.30), residues: 812
  helix:  1.09 (0.27), residues: 386
  sheet: -0.08 (0.45), residues: 117
  loop : -0.93 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP A1353 
   HIS   0.004   0.000   HIS A1312 
   PHE   0.013   0.001   PHE A 764 
   TYR   0.005   0.001   TYR A 953 
   ARG   0.002   0.000   ARG A 969 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.678 
Fit side-chains
  outliers start: 7
  outliers final: 2
  residues processed: 108
  average time/residue: 0.1583
  time to fit residues: 23.7212
Evaluate side-chains
  97 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.689 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0562
  time to fit residues: 1.1553
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   chunk 78 optimal weight:    0.4980
   chunk 48 optimal weight:    0.0040
   chunk 47 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 31 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.8994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 849 ASN
A1172 HIS
** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1312 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6260  Z= 0.180
  Angle     :  0.559  15.349   8502  Z= 0.270
  Chirality :  0.043   0.146   1046
  Planarity :  0.004   0.039   1064
  Dihedral  :  3.619  14.010    854
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 19.53 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.30), residues: 812
  helix:  0.99 (0.27), residues: 387
  sheet: -0.05 (0.45), residues: 115
  loop : -0.93 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A1353 
   HIS   0.011   0.001   HIS A1312 
   PHE   0.014   0.001   PHE A 764 
   TYR   0.006   0.001   TYR A 953 
   ARG   0.001   0.000   ARG A1320 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.720 
Fit side-chains
  outliers start: 14
  outliers final: 6
  residues processed: 106
  average time/residue: 0.1663
  time to fit residues: 24.4502
Evaluate side-chains
  101 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.814 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1175
  time to fit residues: 1.9995
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:   20.0000
   chunk 38 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 61 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   chunk 72 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1312 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6260  Z= 0.175
  Angle     :  0.542   7.059   8502  Z= 0.267
  Chirality :  0.043   0.146   1046
  Planarity :  0.004   0.046   1064
  Dihedral  :  3.628  13.506    854
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 20.86 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.29), residues: 812
  helix:  0.98 (0.27), residues: 388
  sheet:  0.05 (0.45), residues: 116
  loop : -0.98 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP A1353 
   HIS   0.011   0.001   HIS A1312 
   PHE   0.017   0.001   PHE A 764 
   TYR   0.006   0.001   TYR A 953 
   ARG   0.001   0.000   ARG A 969 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.740 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 106
  average time/residue: 0.1615
  time to fit residues: 23.8501
Evaluate side-chains
  102 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.691 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0614
  time to fit residues: 1.4285
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 57 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 47 optimal weight:    7.9990
   chunk 76 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 53 optimal weight:   20.0000
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1312 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6260  Z= 0.176
  Angle     :  0.553   7.387   8502  Z= 0.269
  Chirality :  0.043   0.146   1046
  Planarity :  0.004   0.045   1064
  Dihedral  :  3.645  13.143    854
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 22.04 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.30), residues: 812
  helix:  1.03 (0.27), residues: 387
  sheet:  0.03 (0.45), residues: 116
  loop : -1.03 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A1353 
   HIS   0.012   0.001   HIS A1312 
   PHE   0.017   0.001   PHE A 764 
   TYR   0.007   0.001   TYR A 953 
   ARG   0.001   0.000   ARG A 952 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.812 
Fit side-chains
  outliers start: 4
  outliers final: 1
  residues processed: 101
  average time/residue: 0.1804
  time to fit residues: 25.0645
Evaluate side-chains
  101 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.697 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.3926
  time to fit residues: 1.3717
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 80 optimal weight:    0.0970
   chunk 74 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.9580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 849 ASN
** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1312 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6260  Z= 0.186
  Angle     :  0.568   8.339   8502  Z= 0.275
  Chirality :  0.043   0.156   1046
  Planarity :  0.004   0.045   1064
  Dihedral  :  3.652  12.888    854
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 22.49 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.29), residues: 812
  helix:  0.99 (0.27), residues: 387
  sheet:  0.01 (0.45), residues: 115
  loop : -1.00 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A1353 
   HIS   0.013   0.001   HIS A1312 
   PHE   0.018   0.001   PHE A 764 
   TYR   0.007   0.001   TYR A 953 
   ARG   0.002   0.000   ARG A1320 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.721 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 102
  average time/residue: 0.1726
  time to fit residues: 24.4030
Evaluate side-chains
  100 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.768 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0600
  time to fit residues: 1.1161
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0070
   chunk 66 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 56 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.7804

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1312 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.190810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.142536 restraints weight = 8285.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.146925 restraints weight = 4302.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.149714 restraints weight = 2956.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6260  Z= 0.180
  Angle     :  0.564   8.029   8502  Z= 0.274
  Chirality :  0.043   0.145   1046
  Planarity :  0.004   0.045   1064
  Dihedral  :  3.634  12.588    854
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 22.93 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.29), residues: 812
  helix:  1.03 (0.27), residues: 387
  sheet:  0.15 (0.46), residues: 116
  loop : -1.01 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A1353 
   HIS   0.012   0.001   HIS A1312 
   PHE   0.017   0.001   PHE A 764 
   TYR   0.006   0.001   TYR A 953 
   ARG   0.001   0.000   ARG A 969 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1468.24 seconds
wall clock time: 27 minutes 16.73 seconds (1636.73 seconds total)