Starting phenix.real_space_refine
on Wed Mar  4 10:30:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6kld_0707/03_2026/6kld_0707.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6kld_0707/03_2026/6kld_0707.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6kld_0707/03_2026/6kld_0707.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6kld_0707/03_2026/6kld_0707.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6kld_0707/03_2026/6kld_0707.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6kld_0707/03_2026/6kld_0707.map"
  }
  resolution = 3.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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: 6
    Type Number    sf(0)   Gaussians
     Mn      1      7.51       5
     Zn      1      6.06       5
     S      86      5.16       5
     C    8159      2.51       5
     N    2148      2.21       5
     O    2399      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12794
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 12792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1617, 12792
          Classifications: {'peptide': 1617}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 48, 'TRANS': 1568}
          Chain breaks: 16
          Unresolved non-hydrogen bonds: 163
          Unresolved non-hydrogen angles: 201
          Unresolved non-hydrogen dihedrals: 144
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 8, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 9, 'HIS:plan': 2, 'PHE:plan': 4}
          Unresolved non-hydrogen planarities: 129
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2171  SG  CYS A 284      40.315  69.743  28.123  1.00 52.57           S
  ATOM   2195  SG  CYS A 287      43.390  69.962  25.837  1.00 53.80           S
  ATOM   3474  SG  CYS A 470      39.712  71.589  24.834  1.00 87.91           S

  Time building chain proxies: 2.86, per 1000 atoms: 0.22
  Number of scatterers: 12794
  At special positions: 0
  Unit cell: (114.24, 114.24, 119.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Mn      1     24.99
     S      86     16.00
     O    2399      8.00
     N    2148      7.00
     C    8159      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1691 " - pdb=" SG  CYS A1776 " 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
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 544.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A2302 "
        pdb="ZN    ZN A2302 " - pdb=" ND1 HIS A 472 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A 470 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A 284 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A 287 "
      Number of angles added : 3


  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3080

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 10 sheets defined
      54.1% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 12
      removed outlier: 3.768A  pdb=" N   GLU A   7 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LYS A   9 " --> pdb=" O   VAL A   5 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY A  10 " --> pdb=" O   GLN A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 31
      removed outlier: 3.547A  pdb=" N   GLY A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   THR A  28 " --> pdb=" O   HIS A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 57
      removed outlier: 4.515A  pdb=" N   LEU A  39 " --> pdb=" O   PRO A  35 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   THR A  40 " --> pdb=" O   SER A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 76
      removed outlier: 3.638A  pdb=" N   ILE A  72 " --> pdb=" O   PHE A  68 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ASN A  76 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 133
      removed outlier: 3.510A  pdb=" N   LYS A 122 " --> pdb=" O   ALA A 118 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU A 126 " --> pdb=" O   LYS A 122 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LYS A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   HIS A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   ASP A 129 " --> pdb=" O   ASN A 125 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LYS A 132 " --> pdb=" O   HIS A 128 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   SER A 133 " --> pdb=" O   ASP A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 171
      removed outlier: 3.965A  pdb=" N   ARG A 159 " --> pdb=" O   TRP A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 190
    Processing helix  chain 'A' and resid 214 through 223
      removed outlier: 3.742A  pdb=" N   LEU A 218 " --> pdb=" O   TYR A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 250
      removed outlier: 3.961A  pdb=" N   VAL A 235 " --> pdb=" O   ARG A 231 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ASP A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 274
    Processing helix  chain 'A' and resid 284 through 289
      removed outlier: 3.545A  pdb=" N   ASN A 288 " --> pdb=" O   CYS A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 303
    Processing helix  chain 'A' and resid 322 through 340
      removed outlier: 3.693A  pdb=" N   LEU A 340 " --> pdb=" O   LYS A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 366
    Processing helix  chain 'A' and resid 389 through 391
      No H-bonds generated for 'chain 'A' and resid 389 through 391'
    Processing helix  chain 'A' and resid 396 through 405
    Processing helix  chain 'A' and resid 412 through 421
      removed outlier: 3.584A  pdb=" N   ASN A 416 " --> pdb=" O   ASN A 412 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   CYS A 417 " --> pdb=" O   TRP A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 451
      removed outlier: 3.979A  pdb=" N   LEU A 451 " --> pdb=" O   ILE A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 478
      removed outlier: 3.541A  pdb=" N   MET A 478 " --> pdb=" O   PHE A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 501
    Processing helix  chain 'A' and resid 574 through 578
    Processing helix  chain 'A' and resid 579 through 583
      removed outlier: 4.440A  pdb=" N   PHE A 583 " --> pdb=" O   LEU A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 598
    Processing helix  chain 'A' and resid 605 through 623
      Proline residue:  A 611  - end of helix
    Processing helix  chain 'A' and resid 625 through 644
      removed outlier: 3.639A  pdb=" N   GLN A 629 " --> pdb=" O   SER A 625 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 655
      removed outlier: 3.556A  pdb=" N   LEU A 655 " --> pdb=" O   THR A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 662 through 679
      removed outlier: 4.266A  pdb=" N   VAL A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   VAL A 667 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 701
    Processing helix  chain 'A' and resid 702 through 705
    Processing helix  chain 'A' and resid 712 through 732
      Proline residue:  A 727  - end of helix
    Processing helix  chain 'A' and resid 745 through 760
    Processing helix  chain 'A' and resid 776 through 789
      removed outlier: 3.535A  pdb=" N   ARG A 789 " --> pdb=" O   SER A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 833 through 852
    Processing helix  chain 'A' and resid 864 through 874
      removed outlier: 3.618A  pdb=" N   LEU A 868 " --> pdb=" O   SER A 864 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE A 869 " --> pdb=" O   THR A 865 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ASN A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   THR A 874 " --> pdb=" O   LEU A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 895
    Processing helix  chain 'A' and resid 898 through 921
      removed outlier: 3.652A  pdb=" N   ASP A 921 " --> pdb=" O   ALA A 917 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 961 through 967
      removed outlier: 3.626A  pdb=" N   VAL A 967 " --> pdb=" O   SER A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 971 through 975
    Processing helix  chain 'A' and resid 981 through 989
    Processing helix  chain 'A' and resid 1009 through 1021
    Processing helix  chain 'A' and resid 1024 through 1035
    Processing helix  chain 'A' and resid 1135 through 1156
    Processing helix  chain 'A' and resid 1163 through 1181
    Processing helix  chain 'A' and resid 1197 through 1208
      removed outlier: 3.728A  pdb=" N   PHE A1201 " --> pdb=" O   SER A1197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1221 through 1233
      removed outlier: 3.527A  pdb=" N   LYS A1225 " --> pdb=" O   LEU A1221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1239 through 1249
    Processing helix  chain 'A' and resid 1264 through 1273
    Processing helix  chain 'A' and resid 1295 through 1319
    Processing helix  chain 'A' and resid 1351 through 1365
    Processing helix  chain 'A' and resid 1395 through 1405
      removed outlier: 3.835A  pdb=" N   PHE A1399 " --> pdb=" O   LEU A1395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1411 through 1429
      removed outlier: 3.668A  pdb=" N   ASN A1429 " --> pdb=" O   GLN A1425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1435 through 1450
    Processing helix  chain 'A' and resid 1472 through 1485
    Processing helix  chain 'A' and resid 1488 through 1507
    Processing helix  chain 'A' and resid 1513 through 1520
      removed outlier: 3.778A  pdb=" N   ASN A1517 " --> pdb=" O   GLU A1513 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LEU A1518 " --> pdb=" O   ASN A1514 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLY A1520 " --> pdb=" O   ILE A1516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1523 through 1535
    Processing helix  chain 'A' and resid 1537 through 1545
    Processing helix  chain 'A' and resid 1579 through 1590
      removed outlier: 3.913A  pdb=" N   LYS A1583 " --> pdb=" O   PRO A1579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1614 through 1625
    Processing helix  chain 'A' and resid 1639 through 1645
      removed outlier: 3.733A  pdb=" N   VAL A1643 " --> pdb=" O   TYR A1639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1664 through 1669
      removed outlier: 3.659A  pdb=" N   ASN A1669 " --> pdb=" O   ASN A1666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1678 through 1694
      removed outlier: 3.638A  pdb=" N   GLY A1694 " --> pdb=" O   ALA A1690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1695 through 1699
      removed outlier: 3.861A  pdb=" N   SER A1699 " --> pdb=" O   TRP A1696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1735 through 1744
    Processing helix  chain 'A' and resid 1744 through 1750
    Processing helix  chain 'A' and resid 1758 through 1764
      removed outlier: 3.775A  pdb=" N   SER A1762 " --> pdb=" O   ASP A1758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1777 through 1783
      removed outlier: 3.535A  pdb=" N   MET A1782 " --> pdb=" O   ALA A1778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1787 through 1793
      removed outlier: 3.677A  pdb=" N   HIS A1791 " --> pdb=" O   GLY A1787 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU A1793 " --> pdb=" O   ILE A1789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1805 through 1809
      removed outlier: 3.549A  pdb=" N   ALA A1809 " --> pdb=" O   GLN A1805 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1805 through 1809'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 94
      removed outlier: 6.506A  pdb=" N   LEU A  98 " --> pdb=" O   VAL A 138 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   ILE A 140 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   LEU A 100 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   ASP A 142 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   GLU A 102 " --> pdb=" O   ASP A 142 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   ARG A 144 " --> pdb=" O   GLU A 102 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   PHE A 104 " --> pdb=" O   ARG A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 260
    Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 387
    Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 534
      removed outlier: 6.167A  pdb=" N   LEU A 559 " --> pdb=" O   GLU A 567 " (cutoff:3.500A)
      removed outlier: 5.672A  pdb=" N   GLU A 567 " --> pdb=" O   LEU A 559 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1116 through 1117
      removed outlier: 3.744A  pdb=" N   GLU A1237 " --> pdb=" O   PHE A1117 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1119 through 1122
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1379 through 1380
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1548 through 1549
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1630 through 1631
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1716 through 1719

    612 hydrogen bonds defined for protein.
    1758 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.09

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4135
        1.34 -     1.46: 2880
        1.46 -     1.58: 5874
        1.58 -     1.70: 0
        1.70 -     1.82: 124
  Bond restraints: 13013
  Sorted by residual:
  bond pdb=" CG  GLU A 220 "
       pdb=" CD  GLU A 220 "
    ideal  model  delta    sigma   weight residual
    1.516  1.488  0.028 2.50e-02 1.60e+03 1.22e+00
  bond pdb=" CB  ASP A1488 "
       pdb=" CG  ASP A1488 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.07e+00
  bond pdb=" CA  SER A 950 "
       pdb=" C   SER A 950 "
    ideal  model  delta    sigma   weight residual
    1.525  1.545 -0.020 2.10e-02 2.27e+03 8.79e-01
  bond pdb=" CA  ASP A1488 "
       pdb=" CB  ASP A1488 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.69e-02 3.50e+03 7.36e-01
  bond pdb=" N   ASP A1488 "
       pdb=" CA  ASP A1488 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.011 1.29e-02 6.01e+03 6.66e-01
  ... (remaining 13008 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 17229
        2.00 -     4.00: 271
        4.00 -     6.00: 45
        6.00 -     8.00: 7
        8.00 -    10.00: 2
  Bond angle restraints: 17554
  Sorted by residual:
  angle pdb=" C   ASN A 219 "
        pdb=" N   GLU A 220 "
        pdb=" CA  GLU A 220 "
      ideal   model   delta    sigma   weight residual
     122.38  114.97    7.41 1.81e+00 3.05e-01 1.68e+01
  angle pdb=" C   ASP A 248 "
        pdb=" N   GLU A 249 "
        pdb=" CA  GLU A 249 "
      ideal   model   delta    sigma   weight residual
     122.08  116.53    5.55 1.53e+00 4.27e-01 1.32e+01
  angle pdb=" N   GLU A 220 "
        pdb=" CA  GLU A 220 "
        pdb=" CB  GLU A 220 "
      ideal   model   delta    sigma   weight residual
     110.44  115.30   -4.86 1.53e+00 4.27e-01 1.01e+01
  angle pdb=" N   ILE A1435 "
        pdb=" CA  ILE A1435 "
        pdb=" C   ILE A1435 "
      ideal   model   delta    sigma   weight residual
     111.81  109.12    2.69 8.60e-01 1.35e+00 9.80e+00
  angle pdb=" N   GLU A 249 "
        pdb=" CA  GLU A 249 "
        pdb=" C   GLU A 249 "
      ideal   model   delta    sigma   weight residual
     114.56  110.84    3.72 1.27e+00 6.20e-01 8.59e+00
  ... (remaining 17549 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.25: 7171
       18.25 -    36.51: 619
       36.51 -    54.76: 105
       54.76 -    73.01: 12
       73.01 -    91.27: 14
  Dihedral angle restraints: 7921
    sinusoidal: 3195
      harmonic: 4726
  Sorted by residual:
  dihedral pdb=" CB  CYS A  55 "
           pdb=" SG  CYS A  55 "
           pdb=" SG  CYS A  60 "
           pdb=" CB  CYS A  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    4.33   88.67     1      1.00e+01 1.00e-02 9.38e+01
  dihedral pdb=" CA  ASP A1467 "
           pdb=" C   ASP A1467 "
           pdb=" N   TRP A1468 "
           pdb=" CA  TRP A1468 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.14   22.86     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" CA  ASP A 826 "
           pdb=" C   ASP A 826 "
           pdb=" N   GLU A 827 "
           pdb=" CA  GLU A 827 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.40   21.60     0      5.00e+00 4.00e-02 1.87e+01
  ... (remaining 7918 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1454
       0.041 -    0.082: 454
       0.082 -    0.123: 100
       0.123 -    0.163: 17
       0.163 -    0.204: 2
  Chirality restraints: 2027
  Sorted by residual:
  chirality pdb=" CB  VAL A1465 "
            pdb=" CA  VAL A1465 "
            pdb=" CG1 VAL A1465 "
            pdb=" CG2 VAL A1465 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CG  LEU A 618 "
            pdb=" CB  LEU A 618 "
            pdb=" CD1 LEU A 618 "
            pdb=" CD2 LEU A 618 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.14e-01
  chirality pdb=" CA  ASP A1488 "
            pdb=" N   ASP A1488 "
            pdb=" C   ASP A1488 "
            pdb=" CB  ASP A1488 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.55e-01
  ... (remaining 2024 not shown)

  Planarity restraints: 2219
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A1753 "   -0.029 5.00e-02 4.00e+02   4.39e-02 3.09e+00
        pdb=" N   PRO A1754 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A1754 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A1754 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  36 "    0.029 5.00e-02 4.00e+02   4.27e-02 2.92e+00
        pdb=" N   PRO A  37 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A  37 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  37 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A1488 "    0.007 2.00e-02 2.50e+03   1.47e-02 2.16e+00
        pdb=" C   ASP A1488 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   ASP A1488 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LYS A1489 "    0.008 2.00e-02 2.50e+03
  ... (remaining 2216 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1115
        2.74 -     3.28: 13252
        3.28 -     3.82: 19806
        3.82 -     4.36: 22620
        4.36 -     4.90: 39718
  Nonbonded interactions: 96511
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A1188 "
            pdb="MN    MN A2301 "
     model   vdw
     2.199 2.320
  nonbonded pdb=" ND2 ASN A 788 "
            pdb=" OE1 GLU A1209 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" OE2 GLU A 102 "
            pdb=" NZ  LYS A 122 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" NH1 ARG A 553 "
            pdb=" OH  TYR A 555 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" O   LYS A 757 "
            pdb=" OG  SER A 761 "
     model   vdw
     2.249 3.040
  ... (remaining 96506 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.500
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     13.060
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
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   0.083  13019  Z= 0.154
  Angle     :  0.641  10.003  17561  Z= 0.324
  Chirality :  0.041   0.204   2027
  Planarity :  0.004   0.044   2219
  Dihedral  : 14.001  91.266   4835
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.22 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.21), residues: 1583
  helix:  1.10 (0.19), residues: 821
  sheet: -0.84 (0.51), residues: 95
  loop : -2.65 (0.22), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1473 
 TYR   0.023   0.001   TYR A 701 
 PHE   0.013   0.001   PHE A 286 
 TRP   0.009   0.001   TRP A1717 
 HIS   0.004   0.001   HIS A 472 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (13013)
  covalent geometry    : angle       0.63485 (17554)
  SS BOND              : bond        0.00286 (    2)
  SS BOND              : angle       1.28882 (    4)
  hydrogen bonds       : bond        0.14091 (  612)
  hydrogen bonds       : angle       4.98167 ( 1758)
  metal coordination   : bond        0.07086 (    4)
  metal coordination   : angle       6.68476 (    3)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 0.509 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8554 (p0) cc_final: 0.8195 (p0)
REVERT: A  189 HIS cc_start: 0.8212 (t-90) cc_final: 0.7974 (t70)
REVERT: A  300 PHE cc_start: 0.8810 (m-10) cc_final: 0.8580 (m-10)
REVERT: A  478 MET cc_start: 0.8340 (mtm) cc_final: 0.8126 (mtm)
REVERT: A  639 LEU cc_start: 0.9120 (tp) cc_final: 0.8780 (tp)
REVERT: A  658 GLU cc_start: 0.7516 (pp20) cc_final: 0.7310 (pp20)
REVERT: A  860 LEU cc_start: 0.7457 (pt) cc_final: 0.7200 (pp)
REVERT: A  892 LEU cc_start: 0.8019 (mm) cc_final: 0.7566 (mm)
REVERT: A  958 ILE cc_start: 0.8084 (mt) cc_final: 0.7836 (mt)
REVERT: A  999 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6855 (pm20)
REVERT: A 1097 TYR cc_start: 0.7591 (t80) cc_final: 0.7331 (t80)
REVERT: A 1352 LEU cc_start: 0.9309 (tp) cc_final: 0.9091 (tp)
REVERT: A 1655 CYS cc_start: 0.8117 (m) cc_final: 0.7665 (t)
REVERT: A 1695 GLU cc_start: 0.7313 (pp20) cc_final: 0.7044 (pp20)
REVERT: A 1733 MET cc_start: 0.3958 (tpt) cc_final: 0.3738 (tpt)
REVERT: A 1780 ASP cc_start: 0.7815 (t70) cc_final: 0.7507 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 263
  average time/residue: 0.1012
  time to fit residues: 39.4785
Evaluate side-chains
  207 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.0070
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.6980
   chunk 149 optimal weight:    2.9990
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
A  15 HIS
** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 644 ASN
A 788 ASN
A1496 ASN
A1514 ASN
A1791 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.155975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.121452 restraints weight = 18484.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.123957 restraints weight = 11951.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.125042 restraints weight = 8788.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.125950 restraints weight = 6879.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.126101 restraints weight = 6458.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13019  Z= 0.128
  Angle     :  0.606   9.512  17561  Z= 0.305
  Chirality :  0.040   0.189   2027
  Planarity :  0.004   0.038   2219
  Dihedral  :  4.224  21.183   1715
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.34 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  9.92 %
    Favored  : 88.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.21), residues: 1583
  helix:  1.18 (0.18), residues: 837
  sheet: -0.76 (0.52), residues: 95
  loop : -2.57 (0.22), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1769 
 TYR   0.013   0.001   TYR A 867 
 PHE   0.020   0.001   PHE A1621 
 TRP   0.007   0.001   TRP A1717 
 HIS   0.011   0.001   HIS A 472 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (13013)
  covalent geometry    : angle       0.60500 (17554)
  SS BOND              : bond        0.00300 (    2)
  SS BOND              : angle       1.43364 (    4)
  hydrogen bonds       : bond        0.04206 (  612)
  hydrogen bonds       : angle       4.09701 ( 1758)
  metal coordination   : bond        0.00814 (    4)
  metal coordination   : angle       2.11006 (    3)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 241
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 ASN cc_start: 0.8528 (p0) cc_final: 0.8121 (p0)
REVERT: A  189 HIS cc_start: 0.8304 (t-90) cc_final: 0.7984 (t70)
REVERT: A  300 PHE cc_start: 0.8687 (m-10) cc_final: 0.8456 (m-10)
REVERT: A  639 LEU cc_start: 0.8929 (tp) cc_final: 0.8605 (tp)
REVERT: A  640 MET cc_start: 0.8818 (mmm) cc_final: 0.8601 (mmm)
REVERT: A  650 ASP cc_start: 0.8295 (t0) cc_final: 0.8074 (t0)
REVERT: A  658 GLU cc_start: 0.7667 (pp20) cc_final: 0.7368 (pp20)
REVERT: A  860 LEU cc_start: 0.7520 (pt) cc_final: 0.7297 (pp)
REVERT: A  888 GLU cc_start: 0.7435 (pm20) cc_final: 0.7112 (pm20)
REVERT: A  892 LEU cc_start: 0.8054 (mm) cc_final: 0.7401 (mm)
REVERT: A  999 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7022 (pm20)
REVERT: A 1097 TYR cc_start: 0.7488 (t80) cc_final: 0.7250 (t80)
REVERT: A 1352 LEU cc_start: 0.9139 (tp) cc_final: 0.8932 (tp)
REVERT: A 1393 THR cc_start: 0.8917 (p) cc_final: 0.8671 (p)
REVERT: A 1533 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.6467 (t80)
REVERT: A 1540 GLU cc_start: 0.6813 (mp0) cc_final: 0.6515 (mp0)
REVERT: A 1655 CYS cc_start: 0.8086 (m) cc_final: 0.7561 (t)
REVERT: A 1717 TRP cc_start: 0.8052 (p-90) cc_final: 0.7676 (p-90)
REVERT: A 1771 LYS cc_start: 0.6169 (tptt) cc_final: 0.5885 (tptt)
REVERT: A 1780 ASP cc_start: 0.8209 (t70) cc_final: 0.7927 (t70)
  outliers start: 17
  outliers final: 11
  residues processed: 254
  average time/residue: 0.0960
  time to fit residues: 36.8101
Evaluate side-chains
  221 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 209
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 HIS
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  737 ASN
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  799 LYS
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1484 ILE
Chi-restraints excluded: chain A residue 1533 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0370
   chunk 72 optimal weight:    3.9990
   chunk 117 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0970
   chunk 41 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 130 optimal weight:    1.9990
   chunk 147 optimal weight:    5.9990
   chunk 129 optimal weight:    0.1980
   overall best weight:    0.8660

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

Flipped N/Q/H residues before XYZ refinement:
A 189 HIS
** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 431 HIS
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 800 ASN
A1034 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.148643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.114301 restraints weight = 18622.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.115524 restraints weight = 13144.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.117690 restraints weight = 10218.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.117730 restraints weight = 8422.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.118338 restraints weight = 7898.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13019  Z= 0.131
  Angle     :  0.581  10.027  17561  Z= 0.293
  Chirality :  0.040   0.179   2027
  Planarity :  0.003   0.036   2219
  Dihedral  :  4.131  21.333   1715
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.21 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.03 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.21), residues: 1583
  helix:  1.33 (0.19), residues: 831
  sheet: -0.78 (0.51), residues: 95
  loop : -2.60 (0.22), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 392 
 TYR   0.012   0.001   TYR A 572 
 PHE   0.023   0.001   PHE A1025 
 TRP   0.006   0.001   TRP A1717 
 HIS   0.008   0.001   HIS A 472 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (13013)
  covalent geometry    : angle       0.58069 (17554)
  SS BOND              : bond        0.00350 (    2)
  SS BOND              : angle       1.41070 (    4)
  hydrogen bonds       : bond        0.04007 (  612)
  hydrogen bonds       : angle       3.94876 ( 1758)
  metal coordination   : bond        0.00327 (    4)
  metal coordination   : angle       1.47966 (    3)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 228
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A  146 ASN cc_start: 0.8524 (p0) cc_final: 0.8076 (p0)
REVERT: A  189 HIS cc_start: 0.8230 (t70) cc_final: 0.8002 (t70)
REVERT: A  639 LEU cc_start: 0.9021 (tp) cc_final: 0.8723 (tp)
REVERT: A  640 MET cc_start: 0.8770 (mmm) cc_final: 0.8528 (mmm)
REVERT: A  650 ASP cc_start: 0.8214 (t0) cc_final: 0.7898 (t0)
REVERT: A  654 LYS cc_start: 0.8261 (mmmt) cc_final: 0.8056 (mtpp)
REVERT: A  658 GLU cc_start: 0.7645 (pp20) cc_final: 0.7352 (pp20)
REVERT: A  785 SER cc_start: 0.8641 (m) cc_final: 0.8170 (p)
REVERT: A  888 GLU cc_start: 0.7582 (pm20) cc_final: 0.7228 (pm20)
REVERT: A  892 LEU cc_start: 0.8045 (mm) cc_final: 0.7289 (mm)
REVERT: A  999 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6905 (pm20)
REVERT: A 1018 SER cc_start: 0.9003 (p) cc_final: 0.8802 (p)
REVERT: A 1097 TYR cc_start: 0.7491 (t80) cc_final: 0.7256 (t80)
REVERT: A 1393 THR cc_start: 0.8913 (p) cc_final: 0.8690 (p)
REVERT: A 1540 GLU cc_start: 0.7173 (mp0) cc_final: 0.6782 (mp0)
REVERT: A 1655 CYS cc_start: 0.8194 (m) cc_final: 0.7804 (t)
REVERT: A 1780 ASP cc_start: 0.8174 (t70) cc_final: 0.7884 (t70)
REVERT: A 1782 MET cc_start: 0.7345 (mmm) cc_final: 0.7122 (mmm)
  outliers start: 34
  outliers final: 21
  residues processed: 252
  average time/residue: 0.0897
  time to fit residues: 35.0839
Evaluate side-chains
  224 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 203
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 HIS
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  737 ASN
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  799 LYS
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  989 LYS
Chi-restraints excluded: chain A residue 1160 CYS
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1533 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 139 optimal weight:    3.9990
   chunk 62 optimal weight:    0.2980
   chunk 99 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 143 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 86 optimal weight:   10.0000
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1088 ASN
A1743 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.148821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.113842 restraints weight = 18424.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.115547 restraints weight = 12555.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.116699 restraints weight = 9090.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.117548 restraints weight = 7541.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.117723 restraints weight = 6999.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13019  Z= 0.121
  Angle     :  0.574   8.219  17561  Z= 0.289
  Chirality :  0.040   0.179   2027
  Planarity :  0.003   0.032   2219
  Dihedral  :  4.091  20.772   1715
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.09 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 15.23 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.22), residues: 1583
  helix:  1.40 (0.19), residues: 837
  sheet: -0.77 (0.51), residues: 95
  loop : -2.55 (0.22), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 392 
 TYR   0.012   0.001   TYR A1097 
 PHE   0.018   0.001   PHE A  91 
 TRP   0.008   0.001   TRP A1717 
 HIS   0.006   0.001   HIS A 472 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (13013)
  covalent geometry    : angle       0.57340 (17554)
  SS BOND              : bond        0.00293 (    2)
  SS BOND              : angle       1.43249 (    4)
  hydrogen bonds       : bond        0.03689 (  612)
  hydrogen bonds       : angle       3.83875 ( 1758)
  metal coordination   : bond        0.00456 (    4)
  metal coordination   : angle       1.02002 (    3)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 224
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8523 (p0) cc_final: 0.8071 (p0)
REVERT: A  189 HIS cc_start: 0.8281 (t70) cc_final: 0.8039 (t70)
REVERT: A  215 ASP cc_start: 0.7875 (p0) cc_final: 0.7612 (p0)
REVERT: A  376 ARG cc_start: 0.7671 (mmm-85) cc_final: 0.7419 (mmm-85)
REVERT: A  639 LEU cc_start: 0.8954 (tp) cc_final: 0.8637 (tp)
REVERT: A  640 MET cc_start: 0.8752 (mmm) cc_final: 0.8439 (mmm)
REVERT: A  650 ASP cc_start: 0.8310 (t0) cc_final: 0.7954 (t0)
REVERT: A  658 GLU cc_start: 0.7619 (pp20) cc_final: 0.7300 (pp20)
REVERT: A  827 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7536 (pm20)
REVERT: A  867 TYR cc_start: 0.8707 (t80) cc_final: 0.8389 (t80)
REVERT: A  888 GLU cc_start: 0.7604 (pm20) cc_final: 0.7242 (pm20)
REVERT: A  892 LEU cc_start: 0.8039 (mm) cc_final: 0.7293 (mm)
REVERT: A  999 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6965 (pm20)
REVERT: A 1018 SER cc_start: 0.8804 (p) cc_final: 0.8582 (p)
REVERT: A 1393 THR cc_start: 0.8812 (p) cc_final: 0.8557 (p)
REVERT: A 1466 LYS cc_start: 0.7814 (tmtt) cc_final: 0.7314 (tmtt)
REVERT: A 1540 GLU cc_start: 0.7176 (mp0) cc_final: 0.6755 (mp0)
REVERT: A 1655 CYS cc_start: 0.8314 (m) cc_final: 0.7745 (t)
REVERT: A 1780 ASP cc_start: 0.8211 (t70) cc_final: 0.7967 (t70)
REVERT: A 1782 MET cc_start: 0.7545 (mmm) cc_final: 0.7307 (mmm)
  outliers start: 38
  outliers final: 28
  residues processed: 252
  average time/residue: 0.0890
  time to fit residues: 34.6658
Evaluate side-chains
  231 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 202
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 HIS
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  737 ASN
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  842 SER
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  989 LYS
Chi-restraints excluded: chain A residue 1160 CYS
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1324 SER
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1533 TYR
Chi-restraints excluded: chain A residue 1679 LEU
Chi-restraints excluded: chain A residue 1793 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 43 optimal weight:    0.1980
   chunk 32 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0980
   chunk 67 optimal weight:    2.9990
   chunk 156 optimal weight:    9.9990
   chunk 111 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.148785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.114910 restraints weight = 18534.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.115409 restraints weight = 12943.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.116431 restraints weight = 10070.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.117560 restraints weight = 8398.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.117737 restraints weight = 7369.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13019  Z= 0.130
  Angle     :  0.579   9.847  17561  Z= 0.291
  Chirality :  0.040   0.207   2027
  Planarity :  0.003   0.033   2219
  Dihedral  :  4.068  21.071   1715
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.90 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.95 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.22), residues: 1583
  helix:  1.46 (0.19), residues: 839
  sheet: -0.92 (0.50), residues: 97
  loop : -2.60 (0.22), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 392 
 TYR   0.012   0.001   TYR A 572 
 PHE   0.019   0.001   PHE A  91 
 TRP   0.019   0.001   TRP A1549 
 HIS   0.007   0.001   HIS A1751 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (13013)
  covalent geometry    : angle       0.57887 (17554)
  SS BOND              : bond        0.00330 (    2)
  SS BOND              : angle       1.30452 (    4)
  hydrogen bonds       : bond        0.03737 (  612)
  hydrogen bonds       : angle       3.80181 ( 1758)
  metal coordination   : bond        0.00635 (    4)
  metal coordination   : angle       0.91798 (    3)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 222
  time to evaluate  : 0.572 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8518 (p0) cc_final: 0.8051 (p0)
REVERT: A  189 HIS cc_start: 0.8308 (t70) cc_final: 0.8039 (t70)
REVERT: A  215 ASP cc_start: 0.7844 (p0) cc_final: 0.7629 (p0)
REVERT: A  471 ARG cc_start: 0.7758 (pmt-80) cc_final: 0.6958 (ptt90)
REVERT: A  485 ARG cc_start: 0.8085 (mmm160) cc_final: 0.7801 (mmm160)
REVERT: A  639 LEU cc_start: 0.9035 (tp) cc_final: 0.8724 (tp)
REVERT: A  650 ASP cc_start: 0.8240 (t0) cc_final: 0.7933 (t0)
REVERT: A  658 GLU cc_start: 0.7651 (pp20) cc_final: 0.7332 (pp20)
REVERT: A  785 SER cc_start: 0.8701 (m) cc_final: 0.8208 (p)
REVERT: A  827 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7635 (pm20)
REVERT: A  867 TYR cc_start: 0.8749 (t80) cc_final: 0.8460 (t80)
REVERT: A  888 GLU cc_start: 0.7671 (pm20) cc_final: 0.7307 (pm20)
REVERT: A  892 LEU cc_start: 0.8084 (mm) cc_final: 0.7333 (mm)
REVERT: A  999 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6975 (pm20)
REVERT: A 1393 THR cc_start: 0.8855 (p) cc_final: 0.8612 (p)
REVERT: A 1466 LYS cc_start: 0.7923 (tmtt) cc_final: 0.7444 (tmtt)
REVERT: A 1515 LEU cc_start: 0.7623 (mt) cc_final: 0.7410 (mt)
REVERT: A 1530 PHE cc_start: 0.8546 (m-10) cc_final: 0.8344 (m-80)
REVERT: A 1549 TRP cc_start: 0.7928 (p-90) cc_final: 0.7303 (p-90)
REVERT: A 1782 MET cc_start: 0.7482 (mmm) cc_final: 0.7262 (mmm)
  outliers start: 43
  outliers final: 37
  residues processed: 253
  average time/residue: 0.0928
  time to fit residues: 35.8315
Evaluate side-chains
  244 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 206
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  737 ASN
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  799 LYS
Chi-restraints excluded: chain A residue  800 ASN
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  842 SER
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  989 LYS
Chi-restraints excluded: chain A residue 1108 ILE
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1160 CYS
Chi-restraints excluded: chain A residue 1176 MET
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1324 SER
Chi-restraints excluded: chain A residue 1356 CYS
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1533 TYR
Chi-restraints excluded: chain A residue 1679 LEU
Chi-restraints excluded: chain A residue 1793 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 71 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 112 optimal weight:    0.0270
   chunk 58 optimal weight:    0.0970
   chunk 40 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 136 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1296 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.150493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.115680 restraints weight = 18305.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.117623 restraints weight = 12030.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.118956 restraints weight = 8646.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.119395 restraints weight = 7512.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.119676 restraints weight = 6830.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  13019  Z= 0.111
  Angle     :  0.574   9.497  17561  Z= 0.286
  Chirality :  0.039   0.202   2027
  Planarity :  0.003   0.032   2219
  Dihedral  :  3.972  19.939   1715
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.09 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 18.54 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.22), residues: 1583
  helix:  1.54 (0.19), residues: 843
  sheet: -0.84 (0.50), residues: 97
  loop : -2.56 (0.22), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 392 
 TYR   0.013   0.001   TYR A1097 
 PHE   0.021   0.001   PHE A  91 
 TRP   0.010   0.001   TRP A1549 
 HIS   0.006   0.001   HIS A1751 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (13013)
  covalent geometry    : angle       0.57406 (17554)
  SS BOND              : bond        0.00266 (    2)
  SS BOND              : angle       1.22088 (    4)
  hydrogen bonds       : bond        0.03355 (  612)
  hydrogen bonds       : angle       3.68745 ( 1758)
  metal coordination   : bond        0.00610 (    4)
  metal coordination   : angle       0.74309 (    3)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 232
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8527 (p0) cc_final: 0.8060 (p0)
REVERT: A  189 HIS cc_start: 0.8271 (t70) cc_final: 0.8010 (t70)
REVERT: A  215 ASP cc_start: 0.7839 (p0) cc_final: 0.7128 (t0)
REVERT: A  471 ARG cc_start: 0.7636 (pmt-80) cc_final: 0.6883 (ptt90)
REVERT: A  485 ARG cc_start: 0.7998 (mmm160) cc_final: 0.7734 (mmm160)
REVERT: A  639 LEU cc_start: 0.8980 (tp) cc_final: 0.8686 (tp)
REVERT: A  650 ASP cc_start: 0.8157 (t0) cc_final: 0.7816 (t0)
REVERT: A  658 GLU cc_start: 0.7561 (pp20) cc_final: 0.7273 (pp20)
REVERT: A  782 TYR cc_start: 0.8243 (m-10) cc_final: 0.7889 (m-80)
REVERT: A  785 SER cc_start: 0.8699 (m) cc_final: 0.8201 (p)
REVERT: A  827 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7569 (pm20)
REVERT: A  867 TYR cc_start: 0.8733 (t80) cc_final: 0.8475 (t80)
REVERT: A  888 GLU cc_start: 0.7656 (pm20) cc_final: 0.7292 (pm20)
REVERT: A  892 LEU cc_start: 0.8106 (mm) cc_final: 0.7336 (mm)
REVERT: A  999 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6975 (pm20)
REVERT: A 1393 THR cc_start: 0.8699 (p) cc_final: 0.8474 (p)
REVERT: A 1466 LYS cc_start: 0.7919 (tmtt) cc_final: 0.7404 (tmtt)
REVERT: A 1530 PHE cc_start: 0.8548 (m-10) cc_final: 0.8339 (m-80)
REVERT: A 1549 TRP cc_start: 0.7908 (p-90) cc_final: 0.7167 (p-90)
REVERT: A 1813 ILE cc_start: 0.8255 (mp) cc_final: 0.8014 (tt)
  outliers start: 46
  outliers final: 33
  residues processed: 261
  average time/residue: 0.0895
  time to fit residues: 36.1256
Evaluate side-chains
  245 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 211
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  737 ASN
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  842 SER
Chi-restraints excluded: chain A residue  866 ASP
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1160 CYS
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1533 TYR
Chi-restraints excluded: chain A residue 1679 LEU
Chi-restraints excluded: chain A residue 1793 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0010
   chunk 54 optimal weight:    0.0980
   chunk 117 optimal weight:    3.9990
   chunk 77 optimal weight:    0.3980
   chunk 66 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 135 optimal weight:    5.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.151218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.116299 restraints weight = 18399.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.118893 restraints weight = 13198.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.120047 restraints weight = 9106.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.120510 restraints weight = 7342.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.120761 restraints weight = 6852.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  13019  Z= 0.108
  Angle     :  0.576  10.915  17561  Z= 0.287
  Chirality :  0.039   0.208   2027
  Planarity :  0.003   0.043   2219
  Dihedral  :  3.938  19.206   1715
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.77 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.50 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.22), residues: 1583
  helix:  1.59 (0.19), residues: 837
  sheet: -0.55 (0.51), residues: 87
  loop : -2.47 (0.22), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 392 
 TYR   0.014   0.001   TYR A 558 
 PHE   0.021   0.001   PHE A  91 
 TRP   0.009   0.001   TRP A1549 
 HIS   0.006   0.001   HIS A1751 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (13013)
  covalent geometry    : angle       0.57530 (17554)
  SS BOND              : bond        0.00237 (    2)
  SS BOND              : angle       1.20683 (    4)
  hydrogen bonds       : bond        0.03253 (  612)
  hydrogen bonds       : angle       3.65461 ( 1758)
  metal coordination   : bond        0.00609 (    4)
  metal coordination   : angle       0.60933 (    3)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 225
  time to evaluate  : 0.496 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8539 (p0) cc_final: 0.8070 (p0)
REVERT: A  189 HIS cc_start: 0.8242 (t70) cc_final: 0.7989 (t70)
REVERT: A  215 ASP cc_start: 0.7837 (p0) cc_final: 0.7240 (t0)
REVERT: A  639 LEU cc_start: 0.8923 (tp) cc_final: 0.8641 (tp)
REVERT: A  650 ASP cc_start: 0.8133 (t0) cc_final: 0.7801 (t0)
REVERT: A  658 GLU cc_start: 0.7490 (pp20) cc_final: 0.7191 (pp20)
REVERT: A  782 TYR cc_start: 0.8210 (m-10) cc_final: 0.7983 (m-80)
REVERT: A  827 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7562 (pm20)
REVERT: A  867 TYR cc_start: 0.8721 (t80) cc_final: 0.8441 (t80)
REVERT: A  888 GLU cc_start: 0.7670 (pm20) cc_final: 0.7351 (pm20)
REVERT: A  892 LEU cc_start: 0.8057 (mm) cc_final: 0.7283 (mm)
REVERT: A  999 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6995 (pm20)
REVERT: A 1034 GLN cc_start: 0.7433 (mt0) cc_final: 0.7194 (mt0)
REVERT: A 1466 LYS cc_start: 0.7931 (tmtt) cc_final: 0.7423 (tmtt)
REVERT: A 1549 TRP cc_start: 0.7931 (p-90) cc_final: 0.7163 (p-90)
REVERT: A 1782 MET cc_start: 0.7399 (mmm) cc_final: 0.7037 (mmm)
REVERT: A 1813 ILE cc_start: 0.8241 (mp) cc_final: 0.8001 (tt)
  outliers start: 37
  outliers final: 34
  residues processed: 251
  average time/residue: 0.0888
  time to fit residues: 34.6153
Evaluate side-chains
  252 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 217
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  708 LYS
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  737 ASN
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  842 SER
Chi-restraints excluded: chain A residue  866 ASP
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1533 TYR
Chi-restraints excluded: chain A residue 1679 LEU
Chi-restraints excluded: chain A residue 1773 LEU
Chi-restraints excluded: chain A residue 1793 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 116 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 68 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 144 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 103 optimal weight:    0.8980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.147832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.112591 restraints weight = 18306.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.115134 restraints weight = 12039.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.116278 restraints weight = 8408.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.116740 restraints weight = 7031.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.116955 restraints weight = 6583.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13019  Z= 0.143
  Angle     :  0.608  11.365  17561  Z= 0.302
  Chirality :  0.041   0.221   2027
  Planarity :  0.003   0.046   2219
  Dihedral  :  4.062  20.830   1715
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.84 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 20.33 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.22), residues: 1583
  helix:  1.56 (0.19), residues: 837
  sheet: -0.78 (0.50), residues: 97
  loop : -2.49 (0.22), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 392 
 TYR   0.014   0.001   TYR A1097 
 PHE   0.021   0.001   PHE A1025 
 TRP   0.008   0.001   TRP A1549 
 HIS   0.006   0.001   HIS A 472 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (13013)
  covalent geometry    : angle       0.60750 (17554)
  SS BOND              : bond        0.00350 (    2)
  SS BOND              : angle       1.28036 (    4)
  hydrogen bonds       : bond        0.03725 (  612)
  hydrogen bonds       : angle       3.75497 ( 1758)
  metal coordination   : bond        0.00734 (    4)
  metal coordination   : angle       0.92644 (    3)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 221
  time to evaluate  : 0.507 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8564 (p0) cc_final: 0.8087 (p0)
REVERT: A  189 HIS cc_start: 0.8368 (t70) cc_final: 0.8017 (t70)
REVERT: A  215 ASP cc_start: 0.7864 (p0) cc_final: 0.7132 (t0)
REVERT: A  485 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7726 (mmm160)
REVERT: A  650 ASP cc_start: 0.8298 (t0) cc_final: 0.7939 (t0)
REVERT: A  658 GLU cc_start: 0.7664 (pp20) cc_final: 0.7245 (pp20)
REVERT: A  785 SER cc_start: 0.8747 (m) cc_final: 0.8255 (p)
REVERT: A  827 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7502 (pm20)
REVERT: A  867 TYR cc_start: 0.8802 (t80) cc_final: 0.8539 (t80)
REVERT: A  888 GLU cc_start: 0.7754 (pm20) cc_final: 0.7398 (pm20)
REVERT: A  892 LEU cc_start: 0.8100 (mm) cc_final: 0.7317 (mm)
REVERT: A  999 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6974 (pm20)
REVERT: A 1018 SER cc_start: 0.8919 (p) cc_final: 0.8693 (p)
REVERT: A 1466 LYS cc_start: 0.7908 (tmtt) cc_final: 0.7415 (tmtt)
REVERT: A 1813 ILE cc_start: 0.8266 (mp) cc_final: 0.8037 (tt)
  outliers start: 41
  outliers final: 38
  residues processed: 249
  average time/residue: 0.0926
  time to fit residues: 35.8495
Evaluate side-chains
  255 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 216
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  842 SER
Chi-restraints excluded: chain A residue  866 ASP
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  958 ILE
Chi-restraints excluded: chain A residue 1037 PHE
Chi-restraints excluded: chain A residue 1108 ILE
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1160 CYS
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1242 VAL
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1324 SER
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1533 TYR
Chi-restraints excluded: chain A residue 1679 LEU
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 1773 LEU
Chi-restraints excluded: chain A residue 1793 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 133 optimal weight:    0.7980
   chunk 137 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 130 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 81 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 644 ASN
A1034 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.147416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.112314 restraints weight = 18526.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.114699 restraints weight = 11877.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.115586 restraints weight = 8625.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.116170 restraints weight = 7131.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.116278 restraints weight = 6626.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  13019  Z= 0.148
  Angle     :  0.623  11.938  17561  Z= 0.310
  Chirality :  0.041   0.247   2027
  Planarity :  0.004   0.046   2219
  Dihedral  :  4.114  20.835   1715
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 20.95 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.22), residues: 1583
  helix:  1.57 (0.19), residues: 836
  sheet: -0.74 (0.50), residues: 97
  loop : -2.51 (0.22), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 459 
 TYR   0.014   0.001   TYR A 529 
 PHE   0.021   0.001   PHE A  91 
 TRP   0.009   0.001   TRP A1549 
 HIS   0.005   0.001   HIS A 472 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (13013)
  covalent geometry    : angle       0.62261 (17554)
  SS BOND              : bond        0.00353 (    2)
  SS BOND              : angle       1.29021 (    4)
  hydrogen bonds       : bond        0.03758 (  612)
  hydrogen bonds       : angle       3.78607 ( 1758)
  metal coordination   : bond        0.00651 (    4)
  metal coordination   : angle       1.10117 (    3)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 218
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8598 (p0) cc_final: 0.8106 (p0)
REVERT: A  189 HIS cc_start: 0.8383 (t70) cc_final: 0.8023 (t70)
REVERT: A  215 ASP cc_start: 0.7906 (p0) cc_final: 0.7660 (p0)
REVERT: A  485 ARG cc_start: 0.8035 (mmm160) cc_final: 0.7741 (mmm160)
REVERT: A  640 MET cc_start: 0.8698 (mmm) cc_final: 0.8437 (mmm)
REVERT: A  650 ASP cc_start: 0.8307 (t0) cc_final: 0.7950 (t0)
REVERT: A  658 GLU cc_start: 0.7664 (pp20) cc_final: 0.7255 (pp20)
REVERT: A  785 SER cc_start: 0.8752 (m) cc_final: 0.8275 (p)
REVERT: A  827 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7489 (pm20)
REVERT: A  867 TYR cc_start: 0.8831 (t80) cc_final: 0.8542 (t80)
REVERT: A  888 GLU cc_start: 0.7768 (pm20) cc_final: 0.7401 (pm20)
REVERT: A  892 LEU cc_start: 0.8111 (mm) cc_final: 0.7328 (mm)
REVERT: A  999 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6910 (pm20)
REVERT: A 1018 SER cc_start: 0.8818 (p) cc_final: 0.8529 (p)
REVERT: A 1466 LYS cc_start: 0.7895 (tmtt) cc_final: 0.7392 (tmtt)
REVERT: A 1813 ILE cc_start: 0.8275 (mp) cc_final: 0.8057 (tt)
  outliers start: 42
  outliers final: 39
  residues processed: 247
  average time/residue: 0.0910
  time to fit residues: 35.1324
Evaluate side-chains
  250 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 210
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  799 LYS
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  842 SER
Chi-restraints excluded: chain A residue  866 ASP
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  958 ILE
Chi-restraints excluded: chain A residue 1037 PHE
Chi-restraints excluded: chain A residue 1108 ILE
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1160 CYS
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1242 VAL
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1324 SER
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1472 SER
Chi-restraints excluded: chain A residue 1533 TYR
Chi-restraints excluded: chain A residue 1679 LEU
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 1793 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 80 optimal weight:    0.1980
   chunk 78 optimal weight:    0.9990
   chunk 126 optimal weight:    5.9990
   chunk 118 optimal weight:    6.9990
   chunk 94 optimal weight:    9.9990
   chunk 12 optimal weight:    0.6980
   chunk 160 optimal weight:    0.9980
   chunk 138 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 147 optimal weight:    4.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 901 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.156854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.122525 restraints weight = 18537.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.124300 restraints weight = 11084.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.125757 restraints weight = 8003.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.126098 restraints weight = 6914.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.126466 restraints weight = 6386.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13019  Z= 0.124
  Angle     :  0.614  12.168  17561  Z= 0.303
  Chirality :  0.040   0.266   2027
  Planarity :  0.003   0.041   2219
  Dihedral  :  4.089  20.081   1715
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 21.43 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.22), residues: 1583
  helix:  1.61 (0.19), residues: 838
  sheet: -0.81 (0.50), residues: 97
  loop : -2.49 (0.22), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 376 
 TYR   0.014   0.001   TYR A1097 
 PHE   0.022   0.001   PHE A  91 
 TRP   0.009   0.001   TRP A1549 
 HIS   0.006   0.001   HIS A1751 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (13013)
  covalent geometry    : angle       0.61397 (17554)
  SS BOND              : bond        0.00280 (    2)
  SS BOND              : angle       1.23125 (    4)
  hydrogen bonds       : bond        0.03468 (  612)
  hydrogen bonds       : angle       3.70808 ( 1758)
  metal coordination   : bond        0.00584 (    4)
  metal coordination   : angle       0.78604 (    3)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 221
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8614 (p0) cc_final: 0.8107 (p0)
REVERT: A  189 HIS cc_start: 0.8375 (t70) cc_final: 0.8015 (t70)
REVERT: A  215 ASP cc_start: 0.7873 (p0) cc_final: 0.7137 (t0)
REVERT: A  485 ARG cc_start: 0.8009 (mmm160) cc_final: 0.7690 (mmm160)
REVERT: A  640 MET cc_start: 0.8744 (mmm) cc_final: 0.8486 (mmm)
REVERT: A  650 ASP cc_start: 0.8238 (t0) cc_final: 0.7947 (t0)
REVERT: A  658 GLU cc_start: 0.7620 (pp20) cc_final: 0.7217 (pp20)
REVERT: A  785 SER cc_start: 0.8760 (m) cc_final: 0.8299 (p)
REVERT: A  827 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7477 (pm20)
REVERT: A  867 TYR cc_start: 0.8821 (t80) cc_final: 0.8537 (t80)
REVERT: A  888 GLU cc_start: 0.7747 (pm20) cc_final: 0.7398 (pm20)
REVERT: A  892 LEU cc_start: 0.8125 (mm) cc_final: 0.7332 (mm)
REVERT: A  999 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6980 (pm20)
REVERT: A 1018 SER cc_start: 0.8724 (p) cc_final: 0.8414 (p)
REVERT: A 1466 LYS cc_start: 0.7883 (tmtt) cc_final: 0.7385 (tmtt)
REVERT: A 1813 ILE cc_start: 0.8272 (mp) cc_final: 0.8058 (tt)
  outliers start: 37
  outliers final: 34
  residues processed: 247
  average time/residue: 0.0900
  time to fit residues: 34.3509
Evaluate side-chains
  247 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 212
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  842 SER
Chi-restraints excluded: chain A residue  866 ASP
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1160 CYS
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1242 VAL
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1472 SER
Chi-restraints excluded: chain A residue 1533 TYR
Chi-restraints excluded: chain A residue 1679 LEU
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 1793 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 130 optimal weight:    0.3980
   chunk 98 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 119 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 141 optimal weight:    0.7980
   chunk 129 optimal weight:    0.2980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.155213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.120226 restraints weight = 18613.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.122215 restraints weight = 11412.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.123494 restraints weight = 8181.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.124153 restraints weight = 7021.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.124407 restraints weight = 6406.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13019  Z= 0.122
  Angle     :  0.628  12.166  17561  Z= 0.310
  Chirality :  0.041   0.243   2027
  Planarity :  0.003   0.039   2219
  Dihedral  :  4.077  19.919   1715
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 21.57 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.22), residues: 1583
  helix:  1.62 (0.19), residues: 839
  sheet: -0.85 (0.50), residues: 97
  loop : -2.49 (0.22), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 392 
 TYR   0.013   0.001   TYR A 558 
 PHE   0.022   0.001   PHE A  91 
 TRP   0.009   0.001   TRP A1717 
 HIS   0.006   0.001   HIS A1751 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (13013)
  covalent geometry    : angle       0.62737 (17554)
  SS BOND              : bond        0.00274 (    2)
  SS BOND              : angle       1.23561 (    4)
  hydrogen bonds       : bond        0.03439 (  612)
  hydrogen bonds       : angle       3.71575 ( 1758)
  metal coordination   : bond        0.00498 (    4)
  metal coordination   : angle       0.68909 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1898.69 seconds
wall clock time: 33 minutes 41.99 seconds (2021.99 seconds total)