Starting phenix.real_space_refine
on Fri Feb 14 17:34:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dtd_30851/02_2025/7dtd_30851.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dtd_30851/02_2025/7dtd_30851.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dtd_30851/02_2025/7dtd_30851.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dtd_30851/02_2025/7dtd_30851.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dtd_30851/02_2025/7dtd_30851.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dtd_30851/02_2025/7dtd_30851.cif"
  }
  resolution = 3.3
  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=   0.001 sd=   0.005
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: 4
    Type Number    sf(0)   Gaussians
     S      78      5.16       5
     C    6739      2.51       5
     N    1596      2.21       5
     O    1777      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10190
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 903
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 111, 881
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 107}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 111, 881
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 107}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 871
    Chain: "A"
      Number of atoms: 9192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1138, 9192
          Classifications: {'peptide': 1138}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 1108}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 95
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 95
          Unusual residues: {'9Z9': 1, 'NAG': 4}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 6.27, per 1000 atoms: 0.62
  Number of scatterers: 10190
  At special positions: 0
  Unit cell: (137.238, 139.433, 104.301, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      78     16.00
     O    1777      8.00
     N    1596      7.00
     C    6739      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  53 " - pdb=" SG  CYS B 131 " distance=2.10
    Simple disulfide: pdb=" SG  CYS B  58 " - pdb=" SG  CYS A 919 " distance=2.08
    Simple disulfide: pdb=" SG  CYS A 277 " - pdb=" SG  CYS A 345 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 351 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 921 " - pdb=" SG  CYS A 927 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 959 " - pdb=" SG  CYS A 968 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A1376 " - pdb=" SG  CYS A1396 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1741 " - pdb=" SG  CYS A1756 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 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
  Links applied
    NAG-ASN
      " NAG A2101 " - " ASN A1403 "
      " NAG A2102 " - " ASN A1392 "
      " NAG A2103 " - " ASN A1378 "
      " NAG A2104 " - " ASN A 338 "
  Time building additional restraints: 2.47
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2368

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 4 sheets defined
      68.5% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'B' and resid 122 through 126
    Processing helix  chain 'B' and resid 136 through 139
    Processing helix  chain 'A' and resid 117 through 126
      removed outlier: 4.094A  pdb=" N   ALA A 121 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   VAL A 126 " --> pdb=" O   ILE A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 146
      removed outlier: 3.645A  pdb=" N   SER A 131 " --> pdb=" O   HIS A 127 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   THR A 146 " --> pdb=" O   CYS A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 177
      removed outlier: 3.629A  pdb=" N   LYS A 155 " --> pdb=" O   PRO A 151 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASN A 156 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 205
    Processing helix  chain 'A' and resid 214 through 224
      removed outlier: 4.317A  pdb=" N   THR A 217 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 230
      removed outlier: 3.699A  pdb=" N   VAL A 229 " --> pdb=" O   LYS A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 246
      removed outlier: 4.165A  pdb=" N   LYS A 246 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 269
    Processing helix  chain 'A' and resid 271 through 275
    Processing helix  chain 'A' and resid 368 through 380
    Processing helix  chain 'A' and resid 383 through 396
      removed outlier: 4.013A  pdb=" N   LEU A 387 " --> pdb=" O   PHE A 383 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 439
      removed outlier: 3.593A  pdb=" N   PHE A 403 " --> pdb=" O   TYR A 399 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   PHE A 412 " --> pdb=" O   PHE A 408 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   ILE A 415 " --> pdb=" O   SER A 411 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN A 439 " --> pdb=" O   GLU A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 763
      removed outlier: 4.246A  pdb=" N   VAL A 760 " --> pdb=" O   LYS A 756 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   VAL A 761 " --> pdb=" O   VAL A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 787
      removed outlier: 3.740A  pdb=" N   THR A 775 " --> pdb=" O   ASP A 771 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 819
      removed outlier: 4.638A  pdb=" N   VAL A 799 " --> pdb=" O   HIS A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 831 through 848
      removed outlier: 3.949A  pdb=" N   GLY A 848 " --> pdb=" O   LEU A 844 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 872
      removed outlier: 4.024A  pdb=" N   LEU A 858 " --> pdb=" O   LEU A 855 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   ARG A 862 " --> pdb=" O   ARG A 859 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A 864 " --> pdb=" O   PHE A 861 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ARG A 865 " --> pdb=" O   ARG A 862 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 886
      removed outlier: 3.534A  pdb=" N   ASN A 877 " --> pdb=" O   TRP A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 912
    Processing helix  chain 'A' and resid 914 through 919
    Processing helix  chain 'A' and resid 920 through 923
    Processing helix  chain 'A' and resid 936 through 950
    Processing helix  chain 'A' and resid 953 through 964
      removed outlier: 4.005A  pdb=" N   ASP A 958 " --> pdb=" O   GLU A 954 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   VAL A 962 " --> pdb=" O   ASP A 958 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 995
      removed outlier: 4.175A  pdb=" N   ASN A 980 " --> pdb=" O   MET A 976 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER A 993 " --> pdb=" O   ALA A 989 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE A 995 " --> pdb=" O   LEU A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1203 through 1216
    Processing helix  chain 'A' and resid 1217 through 1234
      removed outlier: 3.860A  pdb=" N   GLU A1221 " --> pdb=" O   HIS A1217 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR A1222 " --> pdb=" O   ASN A1218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1239 through 1245
      removed outlier: 3.560A  pdb=" N   ILE A1242 " --> pdb=" O   ASP A1239 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ASP A1243 " --> pdb=" O   ILE A1240 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ARG A1245 " --> pdb=" O   ILE A1242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1281
      removed outlier: 3.596A  pdb=" N   LYS A1257 " --> pdb=" O   GLU A1253 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   MET A1267 " --> pdb=" O   PHE A1263 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   TYR A1276 " --> pdb=" O   VAL A1272 " (cutoff:3.500A)
      removed outlier: 9.602A  pdb=" N   GLN A1277 " --> pdb=" O   ALA A1273 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   THR A1278 " --> pdb=" O   TYR A1274 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   THR A1281 " --> pdb=" O   GLN A1277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1282 through 1305
      removed outlier: 3.583A  pdb=" N   GLY A1305 " --> pdb=" O   ALA A1301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1311 through 1316
    Processing helix  chain 'A' and resid 1317 through 1327
      Proline residue:  A1323  - end of helix
    Processing helix  chain 'A' and resid 1330 through 1342
      removed outlier: 3.719A  pdb=" N   VAL A1336 " --> pdb=" O   GLY A1332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1343 through 1369
      removed outlier: 3.667A  pdb=" N   ILE A1347 " --> pdb=" O   ALA A1343 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   VAL A1353 " --> pdb=" O   ASN A1349 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE A1361 " --> pdb=" O   PHE A1357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1392 through 1402
    Processing helix  chain 'A' and resid 1417 through 1431
    Processing helix  chain 'A' and resid 1433 through 1443
      removed outlier: 3.816A  pdb=" N   ILE A1437 " --> pdb=" O   GLY A1433 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ASP A1443 " --> pdb=" O   TYR A1439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1456 through 1458
      No H-bonds generated for 'chain 'A' and resid 1456 through 1458'
    Processing helix  chain 'A' and resid 1459 through 1470
      removed outlier: 3.656A  pdb=" N   PHE A1463 " --> pdb=" O   MET A1459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1472 through 1494
      removed outlier: 3.693A  pdb=" N   GLY A1494 " --> pdb=" O   LYS A1490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1503 through 1515
      removed outlier: 3.537A  pdb=" N   MET A1511 " --> pdb=" O   TYR A1507 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LYS A1513 " --> pdb=" O   ASN A1509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1529 through 1540
      removed outlier: 4.002A  pdb=" N   MET A1533 " --> pdb=" O   LYS A1529 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   ARG A1540 " --> pdb=" O   ASP A1536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1540 through 1560
      removed outlier: 3.560A  pdb=" N   ASP A1544 " --> pdb=" O   ARG A1540 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL A1560 " --> pdb=" O   VAL A1556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1566 through 1595
      removed outlier: 3.662A  pdb=" N   ILE A1593 " --> pdb=" O   VAL A1589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1602 through 1621
      removed outlier: 3.724A  pdb=" N   ILE A1606 " --> pdb=" O   ILE A1602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1631 through 1639
    Processing helix  chain 'A' and resid 1642 through 1647
      removed outlier: 4.138A  pdb=" N   ILE A1646 " --> pdb=" O   ARG A1642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1648 through 1652
      removed outlier: 3.954A  pdb=" N   GLY A1652 " --> pdb=" O   LEU A1649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1655 through 1692
      removed outlier: 3.796A  pdb=" N   LEU A1659 " --> pdb=" O   GLY A1655 " (cutoff:3.500A)
      Proline residue:  A1668  - end of helix
      removed outlier: 4.049A  pdb=" N   ASN A1672 " --> pdb=" O   PRO A1668 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE A1673 " --> pdb=" O   ALA A1669 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1709 through 1722
      removed outlier: 3.522A  pdb=" N   GLN A1719 " --> pdb=" O   ILE A1715 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   THR A1722 " --> pdb=" O   PHE A1718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1725 through 1734
      removed outlier: 3.569A  pdb=" N   LEU A1729 " --> pdb=" O   GLY A1725 " (cutoff:3.500A)
      Proline residue:  A1732  - end of helix
    Processing helix  chain 'A' and resid 1758 through 1793
      removed outlier: 4.022A  pdb=" N   GLU A1787 " --> pdb=" O   ALA A1783 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   SER A1790 " --> pdb=" O   LEU A1786 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 44
      removed outlier: 6.418A  pdb=" N   ILE B  41 " --> pdb=" O   GLN B 150 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   VAL B 152 " --> pdb=" O   ILE B  41 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ALA B  43 " --> pdb=" O   VAL B 152 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   GLU B  62 " --> pdb=" O   ASN B  86 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ASN B  86 " --> pdb=" O   GLU B  62 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE B  80 " --> pdb=" O   TRP B  68 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   TYR B  70 " --> pdb=" O   ILE B  78 " (cutoff:3.500A)
      removed outlier: 5.512A  pdb=" N   ILE B  78 " --> pdb=" O   TYR B  70 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   LEU B  79 " --> pdb=" O   LYS B  96 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   LYS B  96 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   GLU B  81 " --> pdb=" O   THR B  94 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 40 through 44
      removed outlier: 6.418A  pdb=" N   ILE B  41 " --> pdb=" O   GLN B 150 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   VAL B 152 " --> pdb=" O   ILE B  41 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ALA B  43 " --> pdb=" O   VAL B 152 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1375 through 1378

    615 hydrogen bonds defined for protein.
    1725 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: 3.24

  Time building geometry restraints manager: 2.91 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 3072
        1.35 -     1.47: 2763
        1.47 -     1.60: 4484
        1.60 -     1.72: 0
        1.72 -     1.85: 127
  Bond restraints: 10446
  Sorted by residual:
  bond pdb=" C1  NAG A2103 "
       pdb=" O5  NAG A2103 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.89e+00
  bond pdb=" CA  GLU A 853 "
       pdb=" C   GLU A 853 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.021 1.34e-02 5.57e+03 2.46e+00
  bond pdb=" CA  LYS B  77 "
       pdb=" C   LYS B  77 "
    ideal  model  delta    sigma   weight residual
    1.520  1.502  0.019 1.22e-02 6.72e+03 2.40e+00
  bond pdb=" C04 9Z9 A2105 "
       pdb=" O72 9Z9 A2105 "
    ideal  model  delta    sigma   weight residual
    1.420  1.389  0.031 2.00e-02 2.50e+03 2.34e+00
  bond pdb=" CA  LEU B 149 "
       pdb=" C   LEU B 149 "
    ideal  model  delta    sigma   weight residual
    1.523  1.505  0.019 1.24e-02 6.50e+03 2.29e+00
  ... (remaining 10441 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 13648
        1.95 -     3.90: 452
        3.90 -     5.85: 63
        5.85 -     7.80: 14
        7.80 -     9.75: 1
  Bond angle restraints: 14178
  Sorted by residual:
  angle pdb=" N   ARG A 322 "
        pdb=" CA  ARG A 322 "
        pdb=" C   ARG A 322 "
      ideal   model   delta    sigma   weight residual
     114.31  107.98    6.33 1.29e+00 6.01e-01 2.40e+01
  angle pdb=" N   TYR A 826 "
        pdb=" CA  TYR A 826 "
        pdb=" C   TYR A 826 "
      ideal   model   delta    sigma   weight residual
     113.02  107.43    5.59 1.20e+00 6.94e-01 2.17e+01
  angle pdb=" N   VAL A 765 "
        pdb=" CA  VAL A 765 "
        pdb=" C   VAL A 765 "
      ideal   model   delta    sigma   weight residual
     106.21  111.13   -4.92 1.07e+00 8.73e-01 2.12e+01
  angle pdb=" N   HIS A1597 "
        pdb=" CA  HIS A1597 "
        pdb=" C   HIS A1597 "
      ideal   model   delta    sigma   weight residual
     114.62  109.40    5.22 1.14e+00 7.69e-01 2.10e+01
  angle pdb=" C   GLY A 854 "
        pdb=" N   LEU A 855 "
        pdb=" CA  LEU A 855 "
      ideal   model   delta    sigma   weight residual
     122.95  115.38    7.57 1.66e+00 3.63e-01 2.08e+01
  ... (remaining 14173 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.99: 5770
       22.99 -    45.99: 415
       45.99 -    68.98: 54
       68.98 -    91.97: 7
       91.97 -   114.97: 1
  Dihedral angle restraints: 6247
    sinusoidal: 2581
      harmonic: 3666
  Sorted by residual:
  dihedral pdb=" CA  ARG A1525 "
           pdb=" C   ARG A1525 "
           pdb=" N   PRO A1526 "
           pdb=" CA  PRO A1526 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.56   28.44     0      5.00e+00 4.00e-02 3.24e+01
  dihedral pdb=" CA  VAL A 765 "
           pdb=" C   VAL A 765 "
           pdb=" N   MET A 766 "
           pdb=" CA  MET A 766 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.36   26.64     0      5.00e+00 4.00e-02 2.84e+01
  dihedral pdb=" CA  LEU A 186 "
           pdb=" C   LEU A 186 "
           pdb=" N   ARG A 187 "
           pdb=" CA  ARG A 187 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.34   25.66     0      5.00e+00 4.00e-02 2.63e+01
  ... (remaining 6244 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1259
       0.051 -    0.103: 324
       0.103 -    0.154: 48
       0.154 -    0.206: 11
       0.206 -    0.257: 7
  Chirality restraints: 1649
  Sorted by residual:
  chirality pdb=" CA AASP B  97 "
            pdb=" N   ASP B  97 "
            pdb=" C   ASP B  97 "
            pdb=" CB AASP B  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CG  LEU A 186 "
            pdb=" CB  LEU A 186 "
            pdb=" CD1 LEU A 186 "
            pdb=" CD2 LEU A 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CA  VAL B  84 "
            pdb=" N   VAL B  84 "
            pdb=" C   VAL B  84 "
            pdb=" CB  VAL B  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.48e+00
  ... (remaining 1646 not shown)

  Planarity restraints: 1731
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 852 "    0.017 2.00e-02 2.50e+03   3.47e-02 1.21e+01
        pdb=" C   VAL A 852 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   VAL A 852 "    0.023 2.00e-02 2.50e+03
        pdb=" N   GLU A 853 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1434 "   -0.013 2.00e-02 2.50e+03   1.51e-02 5.70e+00
        pdb=" CG  TRP A1434 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1434 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1434 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1434 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1434 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1434 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1434 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1434 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1434 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 357 "    0.038 5.00e-02 4.00e+02   5.70e-02 5.19e+00
        pdb=" N   PRO A 358 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 358 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 358 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1728 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 178
        2.67 -     3.22: 10295
        3.22 -     3.78: 15220
        3.78 -     4.34: 20747
        4.34 -     4.90: 33384
  Nonbonded interactions: 79824
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 318 "
            pdb=" CG  GLN A 319 "
     model   vdw
     2.107 3.440
  nonbonded pdb=" O   THR A 793 "
            pdb=" N   PHE A 796 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" OD1 ASN A1410 "
            pdb=" N   VAL A1411 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" O   THR A 793 "
            pdb=" N   HIS A 795 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" O   SER A 856 "
            pdb=" OG  SER A 856 "
     model   vdw
     2.341 3.040
  ... (remaining 79819 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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=0.26 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             0.550
  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:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     25.420
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
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      :  0.004   0.043  10446  Z= 0.269
  Angle     :  0.845   9.753  14178  Z= 0.537
  Chirality :  0.049   0.257   1649
  Planarity :  0.004   0.057   1727
  Dihedral  : 15.192 114.968   3855
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  7.76 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  :  7.06 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -3.18 (0.21), residues: 1242
  helix: -1.36 (0.16), residues: 765
  sheet: -1.22 (0.56), residues: 75
  loop : -3.64 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A1434 
 HIS   0.007   0.001   HIS B 144 
 PHE   0.015   0.001   PHE A 383 
 TYR   0.020   0.001   TYR A 388 
 ARG   0.003   0.000   ARG B 100 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 229
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.8143 (ttp) cc_final: 0.7909 (ttm)
REVERT: A  409 LEU cc_start: 0.8754 (mm) cc_final: 0.8447 (mm)
REVERT: A  424 MET cc_start: 0.8268 (tpt) cc_final: 0.7466 (mtm)
REVERT: A  815 MET cc_start: 0.8228 (tpp) cc_final: 0.8005 (tpp)
REVERT: A  839 ILE cc_start: 0.8471 (mm) cc_final: 0.8263 (mm)
REVERT: A  853 GLU cc_start: 0.0716 (OUTLIER) cc_final: 0.0280 (tm-30)
REVERT: A 1214 ILE cc_start: 0.8713 (mm) cc_final: 0.8496 (mm)
REVERT: A 1219 TRP cc_start: 0.7457 (m-10) cc_final: 0.6982 (m-90)
REVERT: A 1226 PHE cc_start: 0.8248 (t80) cc_final: 0.7956 (t80)
REVERT: A 1267 MET cc_start: 0.8252 (ttp) cc_final: 0.7622 (tmm)
REVERT: A 1277 GLN cc_start: 0.8293 (tp40) cc_final: 0.7265 (mt0)
REVERT: A 1608 ASP cc_start: 0.7872 (t70) cc_final: 0.7463 (t70)
REVERT: A 1665 MET cc_start: 0.6995 (mmt) cc_final: 0.6412 (mmt)
  outliers start: 25
  outliers final: 12
  residues processed: 253
  average time/residue: 0.2032
  time to fit residues: 73.6216
Evaluate side-chains
  180 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 167
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 ASP
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  319 GLN
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  777 CYS
Chi-restraints excluded: chain A residue  793 THR
Chi-restraints excluded: chain A residue  853 GLU
Chi-restraints excluded: chain A residue  918 ASP
Chi-restraints excluded: chain A residue 1378 ASN
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain A residue 1751 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 93 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   chunk 97 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 72 optimal weight:    8.9990
   chunk 112 optimal weight:    4.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN
** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 319 GLN
A 381 GLN
A 416 ASN
A 429 GLN
A 933 HIS
A 980 ASN
A1217 HIS
A1367 ASN
A1375 HIS
A1554 ASN
A1735 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.163392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.120490 restraints weight = 58079.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 5.15
r_work: 0.3425 rms_B_bonded: 5.00 restraints_weight: 2.0000
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3427
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3427 r_free = 0.3427    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3427 r_free = 0.3427    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3427
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10446  Z= 0.253
  Angle     :  0.708  11.720  14178  Z= 0.365
  Chirality :  0.043   0.184   1649
  Planarity :  0.005   0.047   1727
  Dihedral  :  7.913  65.986   1544
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.08 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 13.32 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.34 (0.24), residues: 1242
  helix:  0.10 (0.18), residues: 769
  sheet: -1.05 (0.52), residues: 87
  loop : -2.82 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1434 
 HIS   0.005   0.001   HIS A1393 
 PHE   0.018   0.001   PHE A 256 
 TYR   0.020   0.002   TYR A 825 
 ARG   0.005   0.000   ARG A1639 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 176
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 PHE cc_start: 0.5789 (p90) cc_final: 0.5492 (p90)
REVERT: A  377 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8587 (ttt180)
REVERT: A  424 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7611 (mtm)
REVERT: A  787 MET cc_start: 0.8968 (mtp) cc_final: 0.8718 (mtp)
REVERT: A  918 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7820 (t0)
REVERT: A 1214 ILE cc_start: 0.8715 (mm) cc_final: 0.8514 (mm)
REVERT: A 1219 TRP cc_start: 0.7706 (m-10) cc_final: 0.7125 (m-90)
REVERT: A 1226 PHE cc_start: 0.8551 (t80) cc_final: 0.8270 (t80)
REVERT: A 1266 GLU cc_start: 0.8476 (pp20) cc_final: 0.8195 (pp20)
REVERT: A 1277 GLN cc_start: 0.8365 (tp40) cc_final: 0.7167 (mt0)
REVERT: A 1435 MET cc_start: 0.8365 (mmm) cc_final: 0.8101 (mmp)
REVERT: A 1500 MET cc_start: 0.7818 (mtt) cc_final: 0.7459 (mtp)
REVERT: A 1548 MET cc_start: 0.7729 (mtt) cc_final: 0.7097 (tpp)
REVERT: A 1608 ASP cc_start: 0.8550 (t70) cc_final: 0.8289 (t70)
  outliers start: 35
  outliers final: 22
  residues processed: 198
  average time/residue: 0.2016
  time to fit residues: 58.2383
Evaluate side-chains
  182 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 157
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  775 THR
Chi-restraints excluded: chain A residue  785 MET
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  918 ASP
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain A residue 1616 ILE
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1701 ILE
Chi-restraints excluded: chain A residue 1780 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 1 optimal weight:   20.0000
   chunk 96 optimal weight:   10.0000
   chunk 48 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 2 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 108 optimal weight:    5.9990
   chunk 0 optimal weight:   50.0000
   chunk 122 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 359 ASN
A 759 HIS
A1450 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.162303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.122699 restraints weight = 30378.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 3.55
r_work: 0.3463 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3465
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3465
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10446  Z= 0.267
  Angle     :  0.674   9.423  14178  Z= 0.349
  Chirality :  0.043   0.179   1649
  Planarity :  0.004   0.060   1727
  Dihedral  :  7.274  62.459   1531
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.92 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 16.62 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.72 (0.24), residues: 1242
  helix:  0.58 (0.19), residues: 764
  sheet: -0.82 (0.53), residues: 87
  loop : -2.49 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1434 
 HIS   0.014   0.001   HIS A 759 
 PHE   0.027   0.002   PHE A1466 
 TYR   0.021   0.002   TYR A 388 
 ARG   0.005   0.001   ARG A1402 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 173
  time to evaluate  : 1.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 PHE cc_start: 0.6184 (p90) cc_final: 0.5976 (p90)
REVERT: A  409 LEU cc_start: 0.8930 (mm) cc_final: 0.8655 (mm)
REVERT: A  424 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7527 (mtm)
REVERT: A  766 MET cc_start: 0.6634 (tpt) cc_final: 0.6322 (tpt)
REVERT: A  787 MET cc_start: 0.8849 (mtp) cc_final: 0.8603 (mtp)
REVERT: A  794 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7825 (t0)
REVERT: A  918 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7774 (t0)
REVERT: A 1214 ILE cc_start: 0.8682 (mm) cc_final: 0.8449 (mm)
REVERT: A 1219 TRP cc_start: 0.7614 (m-10) cc_final: 0.7038 (m-90)
REVERT: A 1226 PHE cc_start: 0.8579 (t80) cc_final: 0.8310 (t80)
REVERT: A 1277 GLN cc_start: 0.8358 (tp40) cc_final: 0.7168 (mt0)
REVERT: A 1500 MET cc_start: 0.7587 (mtt) cc_final: 0.7312 (mtp)
REVERT: A 1548 MET cc_start: 0.7728 (mtt) cc_final: 0.7049 (tpp)
REVERT: A 1608 ASP cc_start: 0.8401 (t70) cc_final: 0.8073 (t70)
  outliers start: 47
  outliers final: 32
  residues processed: 203
  average time/residue: 0.2000
  time to fit residues: 60.1941
Evaluate side-chains
  194 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 159
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  775 THR
Chi-restraints excluded: chain A residue  785 MET
Chi-restraints excluded: chain A residue  793 THR
Chi-restraints excluded: chain A residue  794 ASP
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  909 MET
Chi-restraints excluded: chain A residue  918 ASP
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1224 ILE
Chi-restraints excluded: chain A residue 1228 ILE
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1304 LEU
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1379 THR
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1701 ILE
Chi-restraints excluded: chain A residue 1780 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 117 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 78 optimal weight:    8.9990
   chunk 66 optimal weight:    0.6980
   chunk 77 optimal weight:    5.9990
   chunk 80 optimal weight:    3.9990
   chunk 49 optimal weight:    9.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN
** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 272 ASN
A 759 HIS
A 789 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.160775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.117296 restraints weight = 54420.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 4.80
r_work: 0.3381 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3389
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3389
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  10446  Z= 0.307
  Angle     :  0.687   9.174  14178  Z= 0.356
  Chirality :  0.044   0.193   1649
  Planarity :  0.004   0.059   1727
  Dihedral  :  7.134  59.699   1528
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.49 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 17.43 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.59 (0.24), residues: 1242
  helix:  0.63 (0.18), residues: 774
  sheet: -0.62 (0.54), residues: 87
  loop : -2.47 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A1434 
 HIS   0.006   0.001   HIS A1393 
 PHE   0.024   0.002   PHE A1466 
 TYR   0.025   0.002   TYR A 388 
 ARG   0.007   0.001   ARG A1402 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 164
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  278 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8040 (mp)
REVERT: A  424 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.7712 (mtm)
REVERT: A  787 MET cc_start: 0.8941 (mtp) cc_final: 0.8716 (mtp)
REVERT: A  862 ARG cc_start: 0.8169 (ptm-80) cc_final: 0.7733 (ptm-80)
REVERT: A  918 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7855 (t0)
REVERT: A  976 MET cc_start: 0.8555 (ttp) cc_final: 0.8241 (ttp)
REVERT: A 1214 ILE cc_start: 0.8714 (mm) cc_final: 0.8466 (mm)
REVERT: A 1219 TRP cc_start: 0.7662 (m-10) cc_final: 0.7069 (m-90)
REVERT: A 1226 PHE cc_start: 0.8640 (t80) cc_final: 0.8417 (t80)
REVERT: A 1277 GLN cc_start: 0.8340 (tp40) cc_final: 0.7173 (mt0)
REVERT: A 1548 MET cc_start: 0.7816 (mtt) cc_final: 0.7142 (tpp)
REVERT: A 1608 ASP cc_start: 0.8510 (t70) cc_final: 0.8145 (t70)
REVERT: A 1708 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8327 (mt-10)
  outliers start: 64
  outliers final: 41
  residues processed: 207
  average time/residue: 0.2038
  time to fit residues: 61.5094
Evaluate side-chains
  199 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 155
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  400 MET
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  775 THR
Chi-restraints excluded: chain A residue  785 MET
Chi-restraints excluded: chain A residue  793 THR
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  909 MET
Chi-restraints excluded: chain A residue  918 ASP
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1224 ILE
Chi-restraints excluded: chain A residue 1228 ILE
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain A residue 1379 THR
Chi-restraints excluded: chain A residue 1384 ARG
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1701 ILE
Chi-restraints excluded: chain A residue 1780 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0970
   chunk 34 optimal weight:    0.0870
   chunk 105 optimal weight:    8.9990
   chunk 68 optimal weight:    5.9990
   chunk 104 optimal weight:   10.0000
   chunk 41 optimal weight:   20.0000
   chunk 56 optimal weight:    3.9990
   chunk 111 optimal weight:    0.3980
   chunk 113 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN
A 191 ASN
A 272 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.165540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.128161 restraints weight = 45578.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 4.23
r_work: 0.3495 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3499
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3499 r_free = 0.3499    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3499 r_free = 0.3499    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3499
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.103  10446  Z= 0.195
  Angle     :  0.649  10.573  14178  Z= 0.333
  Chirality :  0.041   0.176   1649
  Planarity :  0.004   0.047   1727
  Dihedral  :  6.600  61.351   1528
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.68 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 19.39 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.06 (0.25), residues: 1242
  helix:  1.11 (0.19), residues: 770
  sheet: -0.29 (0.60), residues: 77
  loop : -2.37 (0.32), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1408 
 HIS   0.003   0.001   HIS A1393 
 PHE   0.022   0.001   PHE A 256 
 TYR   0.014   0.001   TYR A 388 
 ARG   0.006   0.000   ARG A1402 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 181
  time to evaluate  : 1.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 MET cc_start: 0.8313 (mmt) cc_final: 0.7843 (mmm)
REVERT: A  409 LEU cc_start: 0.8911 (mm) cc_final: 0.8656 (mm)
REVERT: A  424 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7761 (mtm)
REVERT: A  766 MET cc_start: 0.6432 (tpt) cc_final: 0.6170 (tpt)
REVERT: A  787 MET cc_start: 0.8840 (mtp) cc_final: 0.8599 (mtp)
REVERT: A  816 PHE cc_start: 0.7071 (m-80) cc_final: 0.6809 (m-80)
REVERT: A 1214 ILE cc_start: 0.8715 (mm) cc_final: 0.8457 (mm)
REVERT: A 1219 TRP cc_start: 0.7575 (m-10) cc_final: 0.6965 (m-90)
REVERT: A 1266 GLU cc_start: 0.8420 (pp20) cc_final: 0.8065 (pp20)
REVERT: A 1267 MET cc_start: 0.8522 (tmm) cc_final: 0.8023 (tmm)
REVERT: A 1268 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.7976 (mm)
REVERT: A 1277 GLN cc_start: 0.8335 (tp40) cc_final: 0.7122 (mt0)
REVERT: A 1500 MET cc_start: 0.7652 (mtt) cc_final: 0.7450 (mtp)
REVERT: A 1548 MET cc_start: 0.7788 (mtt) cc_final: 0.7145 (tpp)
REVERT: A 1551 ILE cc_start: 0.8524 (tp) cc_final: 0.8216 (tp)
REVERT: A 1608 ASP cc_start: 0.8364 (t70) cc_final: 0.8041 (t70)
  outliers start: 46
  outliers final: 27
  residues processed: 209
  average time/residue: 0.1886
  time to fit residues: 58.8833
Evaluate side-chains
  188 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 159
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  793 THR
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  909 MET
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1228 ILE
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain A residue 1268 LEU
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1717 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 41 optimal weight:   20.0000
   chunk 1 optimal weight:   30.0000
   chunk 77 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 65 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN
A1577 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.160571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.123179 restraints weight = 51427.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 5.15
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3662
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3662 r_free = 0.3662    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3662 r_free = 0.3662    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3662
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.107  10446  Z= 0.356
  Angle     :  0.726  12.744  14178  Z= 0.371
  Chirality :  0.045   0.200   1649
  Planarity :  0.004   0.046   1727
  Dihedral  :  6.657  58.951   1524
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.33 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 19.03 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.34 (0.24), residues: 1242
  helix:  0.84 (0.18), residues: 782
  sheet: -0.47 (0.60), residues: 77
  loop : -2.43 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A1408 
 HIS   0.007   0.001   HIS A1393 
 PHE   0.025   0.002   PHE A1466 
 TYR   0.025   0.002   TYR A 388 
 ARG   0.003   0.000   ARG A1639 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 161
  time to evaluate  : 1.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  278 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7874 (mp)
REVERT: A  409 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8410 (mm)
REVERT: A  424 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7480 (mtm)
REVERT: A  766 MET cc_start: 0.6937 (tpt) cc_final: 0.6636 (tpt)
REVERT: A  862 ARG cc_start: 0.7840 (ptm-80) cc_final: 0.7403 (ptm-80)
REVERT: A 1214 ILE cc_start: 0.8690 (mm) cc_final: 0.8438 (mm)
REVERT: A 1219 TRP cc_start: 0.7706 (m-10) cc_final: 0.7029 (m-90)
REVERT: A 1267 MET cc_start: 0.8259 (tmm) cc_final: 0.7825 (tmm)
REVERT: A 1277 GLN cc_start: 0.8261 (tp40) cc_final: 0.7957 (tp40)
REVERT: A 1400 ILE cc_start: 0.6671 (OUTLIER) cc_final: 0.6224 (mt)
REVERT: A 1551 ILE cc_start: 0.8610 (tp) cc_final: 0.8389 (tp)
REVERT: A 1608 ASP cc_start: 0.8199 (t70) cc_final: 0.7909 (t70)
REVERT: A 1708 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7599 (mt-10)
  outliers start: 58
  outliers final: 36
  residues processed: 198
  average time/residue: 0.1880
  time to fit residues: 56.0641
Evaluate side-chains
  193 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 153
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  775 THR
Chi-restraints excluded: chain A residue  793 THR
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  909 MET
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1228 ILE
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain A residue 1304 LEU
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain A residue 1379 THR
Chi-restraints excluded: chain A residue 1384 ARG
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain A residue 1400 ILE
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1717 LEU
Chi-restraints excluded: chain A residue 1780 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 73 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 50 optimal weight:    0.4980
   chunk 107 optimal weight:   10.0000
   chunk 108 optimal weight:    2.9990
   chunk 70 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9990
   chunk 104 optimal weight:    0.6980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN
B 144 HIS
A 759 HIS
** A1414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.164899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.121308 restraints weight = 43744.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 4.18
r_work: 0.3471 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3474
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3474 r_free = 0.3474    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3474 r_free = 0.3474    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3474
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10446  Z= 0.174
  Angle     :  0.648  13.977  14178  Z= 0.329
  Chirality :  0.041   0.182   1649
  Planarity :  0.004   0.047   1727
  Dihedral  :  6.150  58.940   1524
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.87 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 21.18 %
    Favored  : 74.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.08 (0.25), residues: 1242
  helix:  1.18 (0.19), residues: 778
  sheet: -0.39 (0.60), residues: 77
  loop : -2.22 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1408 
 HIS   0.006   0.001   HIS A 759 
 PHE   0.026   0.001   PHE A 200 
 TYR   0.014   0.001   TYR A 388 
 ARG   0.003   0.000   ARG A1639 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 170
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 MET cc_start: 0.8347 (mmt) cc_final: 0.7911 (mmm)
REVERT: A  278 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7581 (mp)
REVERT: A  377 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8585 (ttt180)
REVERT: A  424 MET cc_start: 0.8641 (tpt) cc_final: 0.7773 (mtm)
REVERT: A  766 MET cc_start: 0.6697 (tpt) cc_final: 0.6424 (tpt)
REVERT: A  822 MET cc_start: 0.7700 (pmm) cc_final: 0.6627 (ptm)
REVERT: A  862 ARG cc_start: 0.8053 (ptm-80) cc_final: 0.7669 (ptm-80)
REVERT: A 1214 ILE cc_start: 0.8674 (mm) cc_final: 0.8409 (mm)
REVERT: A 1219 TRP cc_start: 0.7598 (m-10) cc_final: 0.6945 (m-90)
REVERT: A 1266 GLU cc_start: 0.8477 (pp20) cc_final: 0.8104 (pp20)
REVERT: A 1270 LYS cc_start: 0.8746 (mtpt) cc_final: 0.8467 (mtmt)
REVERT: A 1277 GLN cc_start: 0.8301 (tp40) cc_final: 0.7051 (mt0)
REVERT: A 1500 MET cc_start: 0.7553 (mtt) cc_final: 0.7352 (mtp)
REVERT: A 1551 ILE cc_start: 0.8596 (tp) cc_final: 0.8377 (tp)
REVERT: A 1608 ASP cc_start: 0.8407 (t70) cc_final: 0.8053 (t70)
REVERT: A 1708 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8161 (mt-10)
  outliers start: 42
  outliers final: 25
  residues processed: 197
  average time/residue: 0.1896
  time to fit residues: 56.0924
Evaluate side-chains
  188 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 161
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  793 THR
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  909 MET
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1228 ILE
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1717 LEU
Chi-restraints excluded: chain A residue 1760 SER
Chi-restraints excluded: chain A residue 1780 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 2 optimal weight:   20.0000
   chunk 33 optimal weight:    5.9990
   chunk 66 optimal weight:    0.7980
   chunk 49 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 77 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   chunk 110 optimal weight:    5.9990
   overall best weight:    3.9588

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN
** A1414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.159468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.121633 restraints weight = 50643.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 4.76
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3640
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3640 r_free = 0.3640    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3640 r_free = 0.3640    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3640
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  10446  Z= 0.369
  Angle     :  0.738  14.931  14178  Z= 0.375
  Chirality :  0.046   0.210   1649
  Planarity :  0.004   0.044   1727
  Dihedral  :  6.453  58.848   1521
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.68 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 20.29 %
    Favored  : 74.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.26 (0.24), residues: 1242
  helix:  0.90 (0.18), residues: 781
  sheet: -0.44 (0.60), residues: 77
  loop : -2.39 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A1408 
 HIS   0.007   0.001   HIS A1393 
 PHE   0.024   0.002   PHE A1466 
 TYR   0.030   0.002   TYR A 388 
 ARG   0.003   0.000   ARG A1639 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 158
  time to evaluate  : 1.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 LEU cc_start: 0.8419 (tt) cc_final: 0.7923 (tp)
REVERT: A  278 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7865 (mp)
REVERT: A  424 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7536 (mtm)
REVERT: A  766 MET cc_start: 0.6809 (tpt) cc_final: 0.6532 (tpt)
REVERT: A  862 ARG cc_start: 0.7866 (ptm-80) cc_final: 0.7443 (ptm-80)
REVERT: A 1214 ILE cc_start: 0.8696 (mm) cc_final: 0.8444 (mm)
REVERT: A 1219 TRP cc_start: 0.7697 (m-10) cc_final: 0.7001 (m-90)
REVERT: A 1266 GLU cc_start: 0.8106 (pp20) cc_final: 0.7868 (pp20)
REVERT: A 1277 GLN cc_start: 0.8261 (tp40) cc_final: 0.7929 (tp40)
REVERT: A 1551 ILE cc_start: 0.8641 (tp) cc_final: 0.8416 (tp)
REVERT: A 1608 ASP cc_start: 0.8151 (t70) cc_final: 0.7842 (t70)
REVERT: A 1708 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7612 (mt-10)
  outliers start: 52
  outliers final: 36
  residues processed: 192
  average time/residue: 0.1868
  time to fit residues: 54.1492
Evaluate side-chains
  191 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 153
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  775 THR
Chi-restraints excluded: chain A residue  793 THR
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  909 MET
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1224 ILE
Chi-restraints excluded: chain A residue 1228 ILE
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1337 VAL
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain A residue 1379 THR
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain A residue 1563 ASP
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1760 SER
Chi-restraints excluded: chain A residue 1780 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 2 optimal weight:   20.0000
   chunk 112 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 120 optimal weight:    9.9990
   chunk 0 optimal weight:   70.0000
   chunk 91 optimal weight:    0.9980
   chunk 66 optimal weight:    8.9990
   chunk 74 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN
** A1414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.161727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.124454 restraints weight = 55604.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 5.41
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3680
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3680
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10446  Z= 0.257
  Angle     :  0.694  14.132  14178  Z= 0.349
  Chirality :  0.043   0.188   1649
  Planarity :  0.004   0.047   1727
  Dihedral  :  6.239  59.959   1521
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.28 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 20.82 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.24), residues: 1242
  helix:  1.20 (0.19), residues: 759
  sheet: -0.40 (0.60), residues: 77
  loop : -2.23 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1408 
 HIS   0.005   0.001   HIS A1393 
 PHE   0.023   0.001   PHE A1466 
 TYR   0.022   0.002   TYR A 388 
 ARG   0.002   0.000   ARG A1639 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 160
  time to evaluate  : 1.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 MET cc_start: 0.8328 (mmt) cc_final: 0.7864 (mmm)
REVERT: A  169 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8313 (p)
REVERT: A  278 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7532 (mp)
REVERT: A  377 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8366 (ttt180)
REVERT: A  424 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7419 (mtm)
REVERT: A  766 MET cc_start: 0.6782 (tpt) cc_final: 0.6547 (tpt)
REVERT: A  862 ARG cc_start: 0.7835 (ptm-80) cc_final: 0.7443 (ptm-80)
REVERT: A  956 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7410 (ttp)
REVERT: A 1214 ILE cc_start: 0.8658 (mm) cc_final: 0.8403 (mm)
REVERT: A 1219 TRP cc_start: 0.7659 (m-10) cc_final: 0.6953 (m-90)
REVERT: A 1266 GLU cc_start: 0.8057 (pp20) cc_final: 0.7794 (pp20)
REVERT: A 1277 GLN cc_start: 0.8176 (tp40) cc_final: 0.7790 (tp40)
REVERT: A 1608 ASP cc_start: 0.8164 (t70) cc_final: 0.7880 (t70)
REVERT: A 1708 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7567 (mt-10)
  outliers start: 49
  outliers final: 32
  residues processed: 189
  average time/residue: 0.1810
  time to fit residues: 51.8464
Evaluate side-chains
  194 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 157
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  793 THR
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  909 MET
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue  956 MET
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue 1228 ILE
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain A residue 1379 THR
Chi-restraints excluded: chain A residue 1384 ARG
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain A residue 1563 ASP
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1717 LEU
Chi-restraints excluded: chain A residue 1760 SER
Chi-restraints excluded: chain A residue 1780 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 50.9392 > 50:
  distance: 36 - 41:  17.882
  distance: 41 - 42:   8.264
  distance: 42 - 43:  11.442
  distance: 42 - 45:  17.314
  distance: 43 - 44:  14.068
  distance: 43 - 50:  14.216
  distance: 45 - 46:  18.710
  distance: 46 - 47:  15.057
  distance: 47 - 48:   8.128
  distance: 47 - 49:  11.231
  distance: 50 - 51:   4.370
  distance: 51 - 52:  13.255
  distance: 52 - 53:  13.586
  distance: 52 - 54:   9.929
  distance: 54 - 55:   8.586
  distance: 55 - 56:  15.489
  distance: 55 - 58:  23.027
  distance: 56 - 57:  27.362
  distance: 56 - 62:   6.741
  distance: 58 - 59:  12.376
  distance: 59 - 60:  30.408
  distance: 59 - 61:  13.219
  distance: 62 - 63:   6.612
  distance: 63 - 64:   6.378
  distance: 63 - 66:   9.987
  distance: 64 - 65:  13.272
  distance: 64 - 68:   7.389
  distance: 65 - 83:  11.026
  distance: 66 - 67:  16.976
  distance: 68 - 69:   6.637
  distance: 69 - 70:   5.637
  distance: 69 - 72:   3.206
  distance: 70 - 71:  10.994
  distance: 70 - 75:   9.484
  distance: 71 - 94:  18.448
  distance: 72 - 73:   7.423
  distance: 72 - 74:   5.210
  distance: 76 - 77:   8.928
  distance: 76 - 79:   6.150
  distance: 77 - 78:   9.215
  distance: 77 - 83:   6.146
  distance: 78 - 100:  11.666
  distance: 79 - 80:   7.763
  distance: 80 - 81:   3.326
  distance: 80 - 82:   5.141
  distance: 83 - 84:   7.916
  distance: 84 - 85:   8.161
  distance: 84 - 87:   6.353
  distance: 85 - 86:  22.835
  distance: 85 - 94:   7.190
  distance: 87 - 88:  10.788
  distance: 88 - 89:   9.153
  distance: 89 - 90:   7.943
  distance: 90 - 91:   6.374
  distance: 91 - 92:   4.140
  distance: 91 - 93:   5.000
  distance: 94 - 95:   5.719
  distance: 95 - 96:   3.697
  distance: 95 - 98:  24.829
  distance: 96 - 97:  17.059
  distance: 96 - 100:   7.577
  distance: 97 - 122:  18.097
  distance: 98 - 99:  24.398
  distance: 100 - 101:   7.756
  distance: 101 - 102:   3.466
  distance: 101 - 104:   7.894
  distance: 102 - 103:  13.788
  distance: 102 - 111:  16.755
  distance: 104 - 105:   5.458
  distance: 105 - 106:   8.293
  distance: 105 - 107:   4.056
  distance: 106 - 108:   5.259
  distance: 107 - 109:   6.769
  distance: 108 - 110:   3.252
  distance: 109 - 110:   3.701
  distance: 111 - 112:   9.693
  distance: 112 - 113:   8.756
  distance: 112 - 115:   8.977
  distance: 113 - 114:  19.405
  distance: 113 - 122:  10.688
  distance: 115 - 116:  10.885
  distance: 116 - 117:   7.236
  distance: 117 - 118:  12.934
  distance: 118 - 119:  10.120
  distance: 119 - 120:   8.062
  distance: 119 - 121:   9.807