Starting phenix.real_space_refine
on Thu Mar  5 03:37:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qd6_13909/03_2026/7qd6_13909.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qd6_13909/03_2026/7qd6_13909.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qd6_13909/03_2026/7qd6_13909.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qd6_13909/03_2026/7qd6_13909.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qd6_13909/03_2026/7qd6_13909.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qd6_13909/03_2026/7qd6_13909.cif"
  }
  resolution = 3.0
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     214      5.49       5
     S      46      5.16       5
     C   11474      2.51       5
     N    3400      2.21       5
     O    3978      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 19112
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 7345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 908, 7345
          Classifications: {'peptide': 908}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 27, 'TRANS': 880}
          Chain breaks: 8
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "B"
      Number of atoms: 1110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 1110
          Classifications: {'DNA': 54}
          Link IDs: {'rna3p': 53}
    Chain: "C"
      Number of atoms: 838
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 838
          Classifications: {'DNA': 41}
          Link IDs: {'rna3p': 40}
    Chain: "G"
      Number of atoms: 263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 263
          Classifications: {'DNA': 13}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 12}
    Chain: "D"
      Number of atoms: 7345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 908, 7345
          Classifications: {'peptide': 908}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 27, 'TRANS': 880}
          Chain breaks: 8
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "E"
      Number of atoms: 1110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 1110
          Classifications: {'DNA': 54}
          Link IDs: {'rna3p': 53}
    Chain: "F"
      Number of atoms: 838
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 838
          Classifications: {'DNA': 41}
          Link IDs: {'rna3p': 40}
    Chain: "H"
      Number of atoms: 263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 263
          Classifications: {'DNA': 13}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 12}
  Time building chain proxies: 3.99, per 1000 atoms: 0.21
  Number of scatterers: 19112
  At special positions: 0
  Unit cell: (167.96, 136.04, 152.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      46     16.00
     P     214     15.00
     O    3978      8.00
     N    3400      7.00
     C   11474      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        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: 1.69
  Conformation dependent library (CDL) restraints added in 645.6 milliseconds
  

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3436

  Finding SS restraints...
    Secondary structure from input PDB file:
      88 helices and 8 sheets defined
      70.2% alpha, 2.1% beta
      98 base pairs and 183 stacking pairs defined.
    Time for finding SS restraints: 2.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 17
    Processing helix  chain 'A' and resid 24 through 29
      removed outlier: 3.623A  pdb=" N   THR A  28 " --> pdb=" O   TRP A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 42
    Processing helix  chain 'A' and resid 45 through 61
      removed outlier: 4.168A  pdb=" N   ARG A  49 " --> pdb=" O   ARG A  45 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   LEU A  50 " --> pdb=" O   GLY A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 85
      removed outlier: 3.628A  pdb=" N   VAL A  77 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL A  80 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.533A  pdb=" N   GLU A  90 " --> pdb=" O   PRO A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 113
      removed outlier: 4.093A  pdb=" N   TRP A 102 " --> pdb=" O   GLY A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 136
      removed outlier: 4.264A  pdb=" N   GLN A 131 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 153
    Processing helix  chain 'A' and resid 159 through 185
      removed outlier: 3.877A  pdb=" N   ILE A 163 " --> pdb=" O   ALA A 159 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   GLY A 185 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 197
    Processing helix  chain 'A' and resid 206 through 213
    Processing helix  chain 'A' and resid 219 through 237
    Processing helix  chain 'A' and resid 246 through 260
    Processing helix  chain 'A' and resid 261 through 268
      removed outlier: 3.553A  pdb=" N   PHE A 268 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 318
      removed outlier: 4.243A  pdb=" N   GLN A 286 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASN A 318 " --> pdb=" O   ILE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 343
    Processing helix  chain 'A' and resid 345 through 354
      removed outlier: 3.638A  pdb=" N   ALA A 349 " --> pdb=" O   ASP A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 369
    Processing helix  chain 'A' and resid 377 through 382
      removed outlier: 3.983A  pdb=" N   ASN A 382 " --> pdb=" O   ASP A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 390
      removed outlier: 3.614A  pdb=" N   VAL A 388 " --> pdb=" O   ARG A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 399
    Processing helix  chain 'A' and resid 407 through 424
    Processing helix  chain 'A' and resid 441 through 446
      removed outlier: 4.118A  pdb=" N   TYR A 446 " --> pdb=" O   GLN A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 472
    Processing helix  chain 'A' and resid 484 through 489
    Processing helix  chain 'A' and resid 511 through 530
      removed outlier: 3.596A  pdb=" N   ILE A 515 " --> pdb=" O   ALA A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 570
      removed outlier: 4.439A  pdb=" N   ALA A 561 " --> pdb=" O   GLU A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 586
    Processing helix  chain 'A' and resid 587 through 592
    Processing helix  chain 'A' and resid 602 through 619
    Processing helix  chain 'A' and resid 621 through 629
    Processing helix  chain 'A' and resid 633 through 645
      removed outlier: 3.557A  pdb=" N   MET A 637 " --> pdb=" O   SER A 633 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ARG A 644 " --> pdb=" O   ALA A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 664
      removed outlier: 3.590A  pdb=" N   GLN A 664 " --> pdb=" O   PHE A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 671
      removed outlier: 4.394A  pdb=" N   TRP A 670 " --> pdb=" O   LEU A 666 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLY A 671 " --> pdb=" O   SER A 667 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 666 through 671'
    Processing helix  chain 'A' and resid 728 through 738
      removed outlier: 3.545A  pdb=" N   VAL A 732 " --> pdb=" O   ASP A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 766
      removed outlier: 3.537A  pdb=" N   PHE A 760 " --> pdb=" O   THR A 756 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ALA A 761 " --> pdb=" O   ASP A 757 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   LEU A 762 " --> pdb=" O   GLN A 758 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   HIS A 764 " --> pdb=" O   PHE A 760 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU A 766 " --> pdb=" O   LEU A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 810
    Processing helix  chain 'A' and resid 810 through 824
    Processing helix  chain 'A' and resid 827 through 834
      removed outlier: 3.599A  pdb=" N   ILE A 831 " --> pdb=" O   SER A 827 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS A 834 " --> pdb=" O   LEU A 830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 866
      removed outlier: 3.746A  pdb=" N   ALA A 845 " --> pdb=" O   GLN A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 891
    Processing helix  chain 'A' and resid 892 through 897
      removed outlier: 3.849A  pdb=" N   GLU A 897 " --> pdb=" O   GLY A 893 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 902 through 938
    Processing helix  chain 'D' and resid 8 through 17
    Processing helix  chain 'D' and resid 24 through 29
      removed outlier: 3.582A  pdb=" N   THR D  28 " --> pdb=" O   TRP D  24 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 33 through 42
    Processing helix  chain 'D' and resid 45 through 61
      removed outlier: 4.152A  pdb=" N   ARG D  49 " --> pdb=" O   ARG D  45 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LEU D  50 " --> pdb=" O   GLY D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 85
      removed outlier: 3.623A  pdb=" N   VAL D  77 " --> pdb=" O   PRO D  73 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   VAL D  80 " --> pdb=" O   VAL D  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 92
      removed outlier: 3.538A  pdb=" N   GLU D  90 " --> pdb=" O   PRO D  87 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU D  92 " --> pdb=" O   GLU D  89 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 113
      removed outlier: 4.131A  pdb=" N   TRP D 102 " --> pdb=" O   GLY D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 136
      removed outlier: 4.368A  pdb=" N   GLN D 131 " --> pdb=" O   GLN D 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 138 through 153
    Processing helix  chain 'D' and resid 159 through 185
      removed outlier: 3.862A  pdb=" N   ILE D 163 " --> pdb=" O   ALA D 159 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   GLY D 185 " --> pdb=" O   ILE D 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 187 through 197
    Processing helix  chain 'D' and resid 201 through 205
      removed outlier: 3.569A  pdb=" N   GLY D 204 " --> pdb=" O   THR D 201 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 206 through 213
    Processing helix  chain 'D' and resid 219 through 237
    Processing helix  chain 'D' and resid 246 through 260
    Processing helix  chain 'D' and resid 261 through 267
    Processing helix  chain 'D' and resid 269 through 318
      removed outlier: 4.223A  pdb=" N   GLN D 286 " --> pdb=" O   LEU D 282 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 318 through 343
    Processing helix  chain 'D' and resid 345 through 354
      removed outlier: 3.877A  pdb=" N   ALA D 349 " --> pdb=" O   ASP D 345 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 355 through 369
    Processing helix  chain 'D' and resid 377 through 382
      removed outlier: 4.008A  pdb=" N   ASN D 382 " --> pdb=" O   ASP D 379 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 384 through 390
      removed outlier: 3.543A  pdb=" N   VAL D 388 " --> pdb=" O   ARG D 384 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 391 through 399
    Processing helix  chain 'D' and resid 407 through 424
    Processing helix  chain 'D' and resid 441 through 446
      removed outlier: 4.177A  pdb=" N   TYR D 446 " --> pdb=" O   GLN D 442 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 453 through 472
    Processing helix  chain 'D' and resid 484 through 489
      removed outlier: 3.530A  pdb=" N   TYR D 488 " --> pdb=" O   ALA D 484 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 511 through 530
    Processing helix  chain 'D' and resid 557 through 570
      removed outlier: 4.445A  pdb=" N   ALA D 561 " --> pdb=" O   GLU D 557 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 575 through 586
    Processing helix  chain 'D' and resid 587 through 592
    Processing helix  chain 'D' and resid 602 through 619
    Processing helix  chain 'D' and resid 621 through 629
    Processing helix  chain 'D' and resid 633 through 645
      removed outlier: 3.521A  pdb=" N   MET D 637 " --> pdb=" O   SER D 633 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ARG D 644 " --> pdb=" O   ALA D 640 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   MET D 645 " --> pdb=" O   SER D 641 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 646 through 664
      removed outlier: 3.654A  pdb=" N   GLN D 664 " --> pdb=" O   PHE D 660 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 666 through 671
      removed outlier: 4.475A  pdb=" N   TRP D 670 " --> pdb=" O   LEU D 666 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY D 671 " --> pdb=" O   SER D 667 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 666 through 671'
    Processing helix  chain 'D' and resid 728 through 738
      removed outlier: 3.590A  pdb=" N   VAL D 732 " --> pdb=" O   ASP D 728 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 756 through 766
      removed outlier: 3.989A  pdb=" N   ALA D 761 " --> pdb=" O   ASP D 757 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   LEU D 762 " --> pdb=" O   GLN D 758 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   HIS D 764 " --> pdb=" O   PHE D 760 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 804 through 824
      removed outlier: 5.179A  pdb=" N   GLU D 812 " --> pdb=" O   LYS D 808 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   ASP D 813 " --> pdb=" O   GLU D 809 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 827 through 834
      removed outlier: 3.587A  pdb=" N   ILE D 831 " --> pdb=" O   SER D 827 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LYS D 834 " --> pdb=" O   LEU D 830 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 841 through 866
      removed outlier: 3.639A  pdb=" N   ALA D 845 " --> pdb=" O   GLN D 841 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 867 through 891
    Processing helix  chain 'D' and resid 902 through 938
    Processing helix  chain 'D' and resid 945 through 949
    Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 403
    Processing sheet with id=AA2, first strand: chain 'A' and resid 573 through 574
      removed outlier: 7.333A  pdb=" N   ILE A 573 " --> pdb=" O   ASN A 958 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 679 through 683
      removed outlier: 3.580A  pdb=" N   THR A 705 " --> pdb=" O   ILE A 722 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE A 722 " --> pdb=" O   THR A 705 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 748 through 750
    Processing sheet with id=AA5, first strand: chain 'D' and resid 401 through 403
    Processing sheet with id=AA6, first strand: chain 'D' and resid 573 through 574
      removed outlier: 7.372A  pdb=" N   ILE D 573 " --> pdb=" O   ASN D 958 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 679 through 683
      removed outlier: 3.559A  pdb=" N   THR D 705 " --> pdb=" O   ILE D 722 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE D 722 " --> pdb=" O   THR D 705 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 748 through 750

    883 hydrogen bonds defined for protein.
    2592 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      244 hydrogen bonds
      488 hydrogen bond angles
      0 basepair planarities
      98 basepair parallelities
      183 stacking parallelities
  Total time for adding SS restraints: 4.29

  Time building geometry restraints manager: 2.14 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4221
        1.33 -     1.46: 5924
        1.46 -     1.58: 9279
        1.58 -     1.71: 424
        1.71 -     1.83: 90
  Bond restraints: 19938
  Sorted by residual:
  bond pdb=" C   GLU A 408 "
       pdb=" N   PRO A 409 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.022 1.28e-02 6.10e+03 2.85e+00
  bond pdb=" CG  LEU D 256 "
       pdb=" CD1 LEU D 256 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.67e+00
  bond pdb=" N   HIS D 969 "
       pdb=" CA  HIS D 969 "
    ideal  model  delta    sigma   weight residual
    1.460  1.483 -0.023 1.42e-02 4.96e+03 2.64e+00
  bond pdb=" SD  MET A 276 "
       pdb=" CE  MET A 276 "
    ideal  model  delta    sigma   weight residual
    1.791  1.751  0.040 2.50e-02 1.60e+03 2.62e+00
  bond pdb=" N   HIS A 969 "
       pdb=" CA  HIS A 969 "
    ideal  model  delta    sigma   weight residual
    1.460  1.483 -0.024 1.54e-02 4.22e+03 2.36e+00
  ... (remaining 19933 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 27275
        2.56 -     5.13: 502
        5.13 -     7.69: 69
        7.69 -    10.26: 23
       10.26 -    12.82: 3
  Bond angle restraints: 27872
  Sorted by residual:
  angle pdb=" C   LYS D 425 "
        pdb=" N   ARG D 426 "
        pdb=" CA  ARG D 426 "
      ideal   model   delta    sigma   weight residual
     121.54  131.36   -9.82 1.91e+00 2.74e-01 2.64e+01
  angle pdb=" N   GLU D 144 "
        pdb=" CA  GLU D 144 "
        pdb=" CB  GLU D 144 "
      ideal   model   delta    sigma   weight residual
     110.28  117.54   -7.26 1.55e+00 4.16e-01 2.20e+01
  angle pdb=" C   LYS A 425 "
        pdb=" N   ARG A 426 "
        pdb=" CA  ARG A 426 "
      ideal   model   delta    sigma   weight residual
     123.91  131.14   -7.23 1.66e+00 3.63e-01 1.89e+01
  angle pdb=" C   GLU D  23 "
        pdb=" N   TRP D  24 "
        pdb=" CA  TRP D  24 "
      ideal   model   delta    sigma   weight residual
     121.54  129.81   -8.27 1.91e+00 2.74e-01 1.87e+01
  angle pdb=" C   GLU A  23 "
        pdb=" N   TRP A  24 "
        pdb=" CA  TRP A  24 "
      ideal   model   delta    sigma   weight residual
     121.54  129.80   -8.26 1.91e+00 2.74e-01 1.87e+01
  ... (remaining 27867 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 8833
       17.88 -    35.76: 1430
       35.76 -    53.63: 870
       53.63 -    71.51: 202
       71.51 -    89.39: 41
  Dihedral angle restraints: 11376
    sinusoidal: 6062
      harmonic: 5314
  Sorted by residual:
  dihedral pdb=" CA  ARG D  45 "
           pdb=" C   ARG D  45 "
           pdb=" N   GLY D  46 "
           pdb=" CA  GLY D  46 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.27  -26.73     0      5.00e+00 4.00e-02 2.86e+01
  dihedral pdb=" CA  MET D 645 "
           pdb=" C   MET D 645 "
           pdb=" N   TYR D 646 "
           pdb=" CA  TYR D 646 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.03   24.97     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  ARG A  45 "
           pdb=" C   ARG A  45 "
           pdb=" N   GLY A  46 "
           pdb=" CA  GLY A  46 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.25  -24.75     0      5.00e+00 4.00e-02 2.45e+01
  ... (remaining 11373 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 2737
       0.072 -    0.145: 325
       0.145 -    0.217: 31
       0.217 -    0.290: 2
       0.290 -    0.362: 1
  Chirality restraints: 3096
  Sorted by residual:
  chirality pdb=" CB  ILE D 452 "
            pdb=" CA  ILE D 452 "
            pdb=" CG1 ILE D 452 "
            pdb=" CG2 ILE D 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.36 2.00e-01 2.50e+01 3.28e+00
  chirality pdb=" CA  GLN A 172 "
            pdb=" N   GLN A 172 "
            pdb=" C   GLN A 172 "
            pdb=" CB  GLN A 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CB  VAL A 759 "
            pdb=" CA  VAL A 759 "
            pdb=" CG1 VAL A 759 "
            pdb=" CG2 VAL A 759 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 3093 not shown)

  Planarity restraints: 2804
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 485 "    0.017 2.00e-02 2.50e+03   2.63e-02 1.21e+01
        pdb=" CG  PHE A 485 "   -0.060 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 485 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 485 "    0.022 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 485 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 485 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 485 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 485 "   -0.015 2.00e-02 2.50e+03   2.26e-02 8.97e+00
        pdb=" CG  PHE D 485 "    0.051 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 485 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 485 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 485 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 485 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 485 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 371 "    0.046 5.00e-02 4.00e+02   6.89e-02 7.59e+00
        pdb=" N   PRO A 372 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A 372 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 372 "    0.038 5.00e-02 4.00e+02
  ... (remaining 2801 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 4201
        2.80 -     3.32: 16701
        3.32 -     3.85: 35673
        3.85 -     4.37: 40616
        4.37 -     4.90: 62985
  Nonbonded interactions: 160176
  Sorted by model distance:
  nonbonded pdb=" O   MET A 614 "
            pdb=" OG1 THR A 618 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OD1 ASP A 734 "
            pdb=" OG  SER A 828 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OE2 GLU D 581 "
            pdb=" OH  TYR D 927 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OH  TYR A 749 "
            pdb=" NE  ARG A 872 "
     model   vdw
     2.317 3.120
  nonbonded pdb=" OD1 ASP D 734 "
            pdb=" OG  SER D 828 "
     model   vdw
     2.322 3.040
  ... (remaining 160171 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.050
  Process input model:                     19.640
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5936
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      :  0.005   0.054  19938  Z= 0.228
  Angle     :  0.887  12.820  27872  Z= 0.481
  Chirality :  0.048   0.362   3096
  Planarity :  0.007   0.069   2804
  Dihedral  : 22.481  89.389   7940
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  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: -0.81 (0.18), residues: 1780
  helix: -0.40 (0.13), residues: 1154
  sheet:  0.12 (0.99), residues: 36
  loop : -0.53 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG D  49 
 TYR   0.036   0.002   TYR D 141 
 PHE   0.060   0.003   PHE A 485 
 TRP   0.029   0.003   TRP D  64 
 HIS   0.017   0.002   HIS D 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (19938)
  covalent geometry    : angle       0.88698 (27872)
  hydrogen bonds       : bond        0.11752 ( 1127)
  hydrogen bonds       : angle       5.49389 ( 3080)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  872 ARG cc_start: 0.5346 (ttp-170) cc_final: 0.4482 (ttt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.5463
  time to fit residues: 111.2133
Evaluate side-chains
  122 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 194 optimal weight:   10.0000
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:   30.0000
   chunk 122 optimal weight:    0.5980
   chunk 91 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A  30 HIS
A 127 GLN
A 131 GLN
A 183 HIS
A 400 HIS
A 481 HIS
A 661 GLN
A 924 ASN
D  43 HIS
D 127 GLN
D 131 GLN
D 525 HIS
D 664 GLN
** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5376 r_free = 0.5376 target = 0.259871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5275 r_free = 0.5275 target = 0.245002 restraints weight = 20598.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.5284 rms_B_bonded: 0.37
r_work: 0.5170 rms_B_bonded: 1.26 restraints_weight: 0.5000
r_work: 0.5152 rms_B_bonded: 1.54 restraints_weight: 0.2500
r_work (final): 0.5152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5488
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  19938  Z= 0.195
  Angle     :  0.622   8.331  27872  Z= 0.351
  Chirality :  0.039   0.161   3096
  Planarity :  0.005   0.055   2804
  Dihedral  : 24.980  98.829   4350
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  9.23 %
    Favored  : 89.42 %
  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:  0.46 (0.19), residues: 1780
  helix:  0.79 (0.15), residues: 1182
  sheet:  0.10 (0.96), residues: 36
  loop : -0.56 (0.26), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 249 
 TYR   0.019   0.002   TYR D 291 
 PHE   0.021   0.002   PHE D 892 
 TRP   0.019   0.002   TRP D 102 
 HIS   0.016   0.002   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (19938)
  covalent geometry    : angle       0.62233 (27872)
  hydrogen bonds       : bond        0.05097 ( 1127)
  hydrogen bonds       : angle       4.06239 ( 3080)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.2901 (ptm) cc_final: 0.2292 (ttp)
REVERT: A  760 PHE cc_start: 0.5508 (OUTLIER) cc_final: 0.4868 (t80)
REVERT: A  872 ARG cc_start: 0.5904 (OUTLIER) cc_final: 0.5349 (mtm180)
REVERT: D  354 MET cc_start: 0.3317 (ppp) cc_final: 0.2628 (ptt)
REVERT: D  388 VAL cc_start: 0.7709 (OUTLIER) cc_final: 0.7260 (m)
REVERT: D  647 ASP cc_start: 0.6940 (m-30) cc_final: 0.6717 (m-30)
  outliers start: 21
  outliers final: 5
  residues processed: 151
  average time/residue: 0.5801
  time to fit residues: 99.3271
Evaluate side-chains
  127 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  760 PHE
Chi-restraints excluded: chain A residue  872 ARG
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  314 ILE
Chi-restraints excluded: chain D residue  388 VAL
Chi-restraints excluded: chain D residue  760 PHE
Chi-restraints excluded: chain D residue  764 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 65 optimal weight:    9.9990
   chunk 145 optimal weight:    4.9990
   chunk 189 optimal weight:    3.9990
   chunk 143 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 175 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 7 optimal weight:    7.9990
   chunk 193 optimal weight:    3.9990
   chunk 188 optimal weight:    0.6980
   overall best weight:    2.4586

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

Flipped N/Q/H residues before XYZ refinement:
A  43 HIS
A 104 HIS
A 127 GLN
A 131 GLN
A 639 ASN
** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 914 ASN
** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 127 GLN
D 131 GLN
D 311 GLN
D 418 HIS
D 639 ASN
** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 914 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5322 r_free = 0.5322 target = 0.252046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.5235 r_free = 0.5235 target = 0.239655 restraints weight = 20529.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.5027 rms_B_bonded: 0.37
r_work: 0.4676 rms_B_bonded: 0.94 restraints_weight: 0.5000
r_work: 0.4448 rms_B_bonded: 1.89 restraints_weight: 0.2500
r_work: 0.4384 rms_B_bonded: 2.63 restraints_weight: 0.1250
r_work (final): 0.4384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6612
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.071  19938  Z= 0.303
  Angle     :  0.734   9.281  27872  Z= 0.406
  Chirality :  0.045   0.247   3096
  Planarity :  0.006   0.055   2804
  Dihedral  : 25.016 102.881   4350
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 13.35 %
    Favored  : 84.13 %
  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 (0.19), residues: 1780
  helix:  0.58 (0.14), residues: 1188
  sheet: -0.12 (0.86), residues: 36
  loop : -0.69 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 635 
 TYR   0.033   0.003   TYR A 141 
 PHE   0.034   0.003   PHE A 592 
 TRP   0.018   0.002   TRP D 102 
 HIS   0.017   0.002   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00687 (19938)
  covalent geometry    : angle       0.73375 (27872)
  hydrogen bonds       : bond        0.07336 ( 1127)
  hydrogen bonds       : angle       4.25565 ( 3080)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 141
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.3583 (ptm) cc_final: 0.2574 (ttp)
REVERT: A  250 LEU cc_start: 0.7362 (mt) cc_final: 0.7119 (tp)
REVERT: A  760 PHE cc_start: 0.5702 (OUTLIER) cc_final: 0.4582 (t80)
REVERT: A  872 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5818 (mtm180)
REVERT: D  160 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6955 (tpp)
REVERT: D  647 ASP cc_start: 0.6850 (m-30) cc_final: 0.6517 (m-30)
REVERT: D  832 MET cc_start: 0.5674 (tpp) cc_final: 0.5275 (ttm)
  outliers start: 39
  outliers final: 14
  residues processed: 161
  average time/residue: 0.5767
  time to fit residues: 105.9424
Evaluate side-chains
  145 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  569 MET
Chi-restraints excluded: chain A residue  681 MET
Chi-restraints excluded: chain A residue  760 PHE
Chi-restraints excluded: chain A residue  872 ARG
Chi-restraints excluded: chain D residue  160 MET
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  314 ILE
Chi-restraints excluded: chain D residue  335 THR
Chi-restraints excluded: chain D residue  363 VAL
Chi-restraints excluded: chain D residue  388 VAL
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  568 SER
Chi-restraints excluded: chain D residue  681 MET
Chi-restraints excluded: chain D residue  760 PHE
Chi-restraints excluded: chain D residue  764 HIS
Chi-restraints excluded: chain D residue  851 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 153 optimal weight:    0.4980
   chunk 22 optimal weight:    0.7980
   chunk 132 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 178 optimal weight:    5.9990
   chunk 84 optimal weight:    0.6980
   chunk 167 optimal weight:    5.9990
   chunk 122 optimal weight:    0.6980
   chunk 136 optimal weight:    0.8980
   chunk 118 optimal weight:    0.9990
   chunk 49 optimal weight:   20.0000
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  43 HIS
A 127 GLN
A 203 ASN
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 810 ASN
D  43 HIS
** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 203 ASN
D 311 GLN
D 661 GLN
** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 924 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5365 r_free = 0.5365 target = 0.256880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.5276 r_free = 0.5276 target = 0.243997 restraints weight = 20593.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.5285 rms_B_bonded: 0.32
r_work: 0.5131 rms_B_bonded: 0.85 restraints_weight: 0.5000
r_work: 0.5101 rms_B_bonded: 1.35 restraints_weight: 0.2500
r_work: 0.4946 rms_B_bonded: 4.82 restraints_weight: 0.1250
r_work (final): 0.4946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5886
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  19938  Z= 0.151
  Angle     :  0.574   9.095  27872  Z= 0.326
  Chirality :  0.037   0.157   3096
  Planarity :  0.004   0.045   2804
  Dihedral  : 24.910 107.413   4350
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 15.29 %
    Favored  : 82.19 %
  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:  0.94 (0.20), residues: 1780
  helix:  1.24 (0.15), residues: 1186
  sheet:  0.06 (0.88), residues: 36
  loop : -0.57 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 942 
 TYR   0.025   0.002   TYR D 492 
 PHE   0.017   0.002   PHE D 117 
 TRP   0.022   0.001   TRP A 102 
 HIS   0.015   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (19938)
  covalent geometry    : angle       0.57355 (27872)
  hydrogen bonds       : bond        0.04367 ( 1127)
  hydrogen bonds       : angle       3.84380 ( 3080)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 140
  time to evaluate  : 0.677 
Fit side-chains
REVERT: A  153 MET cc_start: 0.2942 (ptm) cc_final: 0.2146 (ttp)
REVERT: A  250 LEU cc_start: 0.7115 (mt) cc_final: 0.6817 (tp)
REVERT: A  359 MET cc_start: 0.5419 (tpt) cc_final: 0.5180 (tpp)
REVERT: A  669 TYR cc_start: 0.5683 (m-10) cc_final: 0.5451 (m-10)
REVERT: A  872 ARG cc_start: 0.5786 (OUTLIER) cc_final: 0.5481 (mtm180)
REVERT: D  203 ASN cc_start: 0.3728 (OUTLIER) cc_final: 0.3057 (m-40)
REVERT: D  354 MET cc_start: 0.3497 (ppp) cc_final: 0.2765 (ptt)
REVERT: D  647 ASP cc_start: 0.6997 (m-30) cc_final: 0.6758 (m-30)
  outliers start: 39
  outliers final: 9
  residues processed: 166
  average time/residue: 0.5432
  time to fit residues: 103.2872
Evaluate side-chains
  138 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  384 ARG
Chi-restraints excluded: chain A residue  681 MET
Chi-restraints excluded: chain A residue  872 ARG
Chi-restraints excluded: chain A residue  944 ASP
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain D residue  324 GLU
Chi-restraints excluded: chain D residue  388 VAL
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  760 PHE
Chi-restraints excluded: chain D residue  764 HIS
Chi-restraints excluded: chain D residue  851 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 134 optimal weight:    0.6980
   chunk 130 optimal weight:    2.9990
   chunk 128 optimal weight:    1.9990
   chunk 121 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 107 optimal weight:    0.6980
   chunk 158 optimal weight:    1.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 203 ASN
** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5343 r_free = 0.5343 target = 0.254482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.5282 r_free = 0.5282 target = 0.245728 restraints weight = 20527.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.5288 rms_B_bonded: 0.22
r_work: 0.5012 rms_B_bonded: 0.63 restraints_weight: 0.5000
r_work: 0.4940 rms_B_bonded: 1.58 restraints_weight: 0.2500
r_work: 0.4904 rms_B_bonded: 2.13 restraints_weight: 0.1250
r_work (final): 0.4904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6069
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  19938  Z= 0.208
  Angle     :  0.614   9.747  27872  Z= 0.346
  Chirality :  0.040   0.240   3096
  Planarity :  0.004   0.046   2804
  Dihedral  : 24.894 110.133   4350
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 16.77 %
    Favored  : 80.52 %
  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:  0.86 (0.20), residues: 1780
  helix:  1.21 (0.15), residues: 1184
  sheet: -0.26 (0.82), residues: 36
  loop : -0.65 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 635 
 TYR   0.032   0.002   TYR A 141 
 PHE   0.032   0.002   PHE A 128 
 TRP   0.021   0.002   TRP A 102 
 HIS   0.013   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (19938)
  covalent geometry    : angle       0.61360 (27872)
  hydrogen bonds       : bond        0.05399 ( 1127)
  hydrogen bonds       : angle       3.89835 ( 3080)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 133
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A  153 MET cc_start: 0.3144 (ptm) cc_final: 0.2286 (ttp)
REVERT: A  359 MET cc_start: 0.5672 (tpt) cc_final: 0.5363 (tpp)
REVERT: D  203 ASN cc_start: 0.3512 (OUTLIER) cc_final: 0.2971 (m-40)
REVERT: D  311 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6189 (tt0)
REVERT: D  622 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6407 (mt)
REVERT: D  647 ASP cc_start: 0.6753 (m-30) cc_final: 0.6518 (m-30)
  outliers start: 42
  outliers final: 20
  residues processed: 162
  average time/residue: 0.5355
  time to fit residues: 99.5856
Evaluate side-chains
  150 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  384 ARG
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  569 MET
Chi-restraints excluded: chain A residue  681 MET
Chi-restraints excluded: chain A residue  810 ASN
Chi-restraints excluded: chain A residue  944 ASP
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  311 GLN
Chi-restraints excluded: chain D residue  314 ILE
Chi-restraints excluded: chain D residue  324 GLU
Chi-restraints excluded: chain D residue  335 THR
Chi-restraints excluded: chain D residue  388 VAL
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  622 LEU
Chi-restraints excluded: chain D residue  760 PHE
Chi-restraints excluded: chain D residue  764 HIS
Chi-restraints excluded: chain D residue  851 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 123 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 92 optimal weight:    1.9990
   chunk 154 optimal weight:    1.9990
   chunk 157 optimal weight:    1.9990
   chunk 110 optimal weight:    9.9990
   chunk 73 optimal weight:    9.9990
   chunk 162 optimal weight:    2.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  48 ASN
D 104 HIS
D 203 ASN
D 311 GLN
** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5326 r_free = 0.5326 target = 0.253373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.5265 r_free = 0.5265 target = 0.244563 restraints weight = 20345.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.5270 rms_B_bonded: 0.22
r_work: 0.5006 rms_B_bonded: 0.59 restraints_weight: 0.5000
r_work: 0.4944 rms_B_bonded: 1.32 restraints_weight: 0.2500
r_work: 0.4884 rms_B_bonded: 2.28 restraints_weight: 0.1250
r_work (final): 0.4884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6103
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  19938  Z= 0.250
  Angle     :  0.658   8.121  27872  Z= 0.368
  Chirality :  0.042   0.243   3096
  Planarity :  0.005   0.047   2804
  Dihedral  : 24.920 112.108   4350
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 17.68 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.63 (0.20), residues: 1780
  helix:  1.03 (0.15), residues: 1184
  sheet: -0.56 (0.78), residues: 36
  loop : -0.73 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 635 
 TYR   0.022   0.002   TYR A 492 
 PHE   0.024   0.002   PHE A 592 
 TRP   0.022   0.002   TRP A 102 
 HIS   0.013   0.002   HIS D 748 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 (19938)
  covalent geometry    : angle       0.65832 (27872)
  hydrogen bonds       : bond        0.06031 ( 1127)
  hydrogen bonds       : angle       3.99287 ( 3080)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 135
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.3227 (ptm) cc_final: 0.2350 (ttp)
REVERT: A  359 MET cc_start: 0.5590 (tpt) cc_final: 0.5294 (tpp)
REVERT: A  597 THR cc_start: 0.7024 (OUTLIER) cc_final: 0.6424 (p)
REVERT: D  300 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7700 (mmp)
REVERT: D  354 MET cc_start: 0.3808 (ppp) cc_final: 0.2632 (ptt)
REVERT: D  647 ASP cc_start: 0.6763 (m-30) cc_final: 0.6537 (m-30)
REVERT: D  669 TYR cc_start: 0.5676 (m-10) cc_final: 0.5429 (m-10)
REVERT: D  832 MET cc_start: 0.5545 (OUTLIER) cc_final: 0.5333 (ttm)
  outliers start: 51
  outliers final: 22
  residues processed: 171
  average time/residue: 0.5591
  time to fit residues: 108.8060
Evaluate side-chains
  156 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  384 ARG
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  569 MET
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  681 MET
Chi-restraints excluded: chain A residue  750 THR
Chi-restraints excluded: chain A residue  810 ASN
Chi-restraints excluded: chain A residue  944 ASP
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue   44 ARG
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  300 MET
Chi-restraints excluded: chain D residue  314 ILE
Chi-restraints excluded: chain D residue  324 GLU
Chi-restraints excluded: chain D residue  335 THR
Chi-restraints excluded: chain D residue  388 VAL
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  568 SER
Chi-restraints excluded: chain D residue  760 PHE
Chi-restraints excluded: chain D residue  764 HIS
Chi-restraints excluded: chain D residue  832 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 161 optimal weight:    0.6980
   chunk 107 optimal weight:    0.7980
   chunk 132 optimal weight:    2.9990
   chunk 192 optimal weight:    0.9990
   chunk 84 optimal weight:    0.5980
   chunk 130 optimal weight:    0.9990
   chunk 126 optimal weight:    0.1980
   chunk 58 optimal weight:    0.0070
   chunk 198 optimal weight:    0.9980
   chunk 118 optimal weight:    0.9980
   chunk 4 optimal weight:   20.0000
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 810 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5370 r_free = 0.5370 target = 0.258843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.5279 r_free = 0.5279 target = 0.245349 restraints weight = 20674.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.5288 rms_B_bonded: 0.32
r_work: 0.5152 rms_B_bonded: 1.10 restraints_weight: 0.5000
r_work: 0.5129 rms_B_bonded: 1.48 restraints_weight: 0.2500
r_work (final): 0.5129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5571
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  19938  Z= 0.141
  Angle     :  0.559   9.357  27872  Z= 0.318
  Chirality :  0.037   0.154   3096
  Planarity :  0.004   0.044   2804
  Dihedral  : 24.918 120.349   4350
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 18.84 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.21 (0.20), residues: 1780
  helix:  1.53 (0.15), residues: 1182
  sheet: -0.16 (0.83), residues: 36
  loop : -0.62 (0.26), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 942 
 TYR   0.033   0.001   TYR A 141 
 PHE   0.027   0.002   PHE A 892 
 TRP   0.024   0.001   TRP A 102 
 HIS   0.013   0.001   HIS D 748 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (19938)
  covalent geometry    : angle       0.55936 (27872)
  hydrogen bonds       : bond        0.04016 ( 1127)
  hydrogen bonds       : angle       3.69029 ( 3080)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 0.642 
Fit side-chains
REVERT: A  153 MET cc_start: 0.2957 (ptm) cc_final: 0.2209 (ttp)
REVERT: A  388 VAL cc_start: 0.7416 (OUTLIER) cc_final: 0.7164 (p)
REVERT: D  311 GLN cc_start: 0.6598 (OUTLIER) cc_final: 0.6090 (tt0)
REVERT: D  354 MET cc_start: 0.3117 (ppp) cc_final: 0.2295 (ptt)
REVERT: D  647 ASP cc_start: 0.6824 (m-30) cc_final: 0.6593 (m-30)
REVERT: D  832 MET cc_start: 0.5351 (tpp) cc_final: 0.5048 (ttm)
REVERT: D  979 LEU cc_start: 0.6193 (OUTLIER) cc_final: 0.5897 (mp)
  outliers start: 33
  outliers final: 16
  residues processed: 157
  average time/residue: 0.5413
  time to fit residues: 97.1096
Evaluate side-chains
  140 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  384 ARG
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  681 MET
Chi-restraints excluded: chain A residue  810 ASN
Chi-restraints excluded: chain A residue  944 ASP
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  311 GLN
Chi-restraints excluded: chain D residue  324 GLU
Chi-restraints excluded: chain D residue  388 VAL
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  663 GLU
Chi-restraints excluded: chain D residue  731 HIS
Chi-restraints excluded: chain D residue  760 PHE
Chi-restraints excluded: chain D residue  764 HIS
Chi-restraints excluded: chain D residue  979 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 161 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 106 optimal weight:   10.0000
   chunk 180 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 195 optimal weight:   10.0000
   chunk 164 optimal weight:    0.0170
   chunk 9 optimal weight:   30.0000
   chunk 79 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 117 optimal weight:    0.6980
   overall best weight:    1.7424

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

Flipped N/Q/H residues before XYZ refinement:
A  48 ASN
** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 764 HIS
D 203 ASN
** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 810 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5327 r_free = 0.5327 target = 0.253049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.5243 r_free = 0.5243 target = 0.241068 restraints weight = 20490.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.5253 rms_B_bonded: 0.35
r_work: 0.5100 rms_B_bonded: 0.87 restraints_weight: 0.5000
r_work: 0.5070 rms_B_bonded: 1.37 restraints_weight: 0.2500
r_work: 0.4907 rms_B_bonded: 4.96 restraints_weight: 0.1250
r_work (final): 0.4907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5980
moved from start:          0.3376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  19938  Z= 0.231
  Angle     :  0.645   9.976  27872  Z= 0.360
  Chirality :  0.041   0.212   3096
  Planarity :  0.005   0.058   2804
  Dihedral  : 24.884 121.042   4350
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 19.61 %
    Favored  : 77.68 %
  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:  0.81 (0.20), residues: 1780
  helix:  1.19 (0.15), residues: 1190
  sheet: -0.40 (0.82), residues: 36
  loop : -0.75 (0.27), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 635 
 TYR   0.024   0.002   TYR A 492 
 PHE   0.025   0.002   PHE A 592 
 TRP   0.022   0.002   TRP A 102 
 HIS   0.015   0.002   HIS A 748 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 (19938)
  covalent geometry    : angle       0.64503 (27872)
  hydrogen bonds       : bond        0.05856 ( 1127)
  hydrogen bonds       : angle       3.91117 ( 3080)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 128
  time to evaluate  : 0.449 
Fit side-chains
REVERT: A  153 MET cc_start: 0.3078 (ptm) cc_final: 0.2272 (ttp)
REVERT: A  388 VAL cc_start: 0.7563 (OUTLIER) cc_final: 0.7323 (p)
REVERT: A  760 PHE cc_start: 0.5718 (OUTLIER) cc_final: 0.4715 (t80)
REVERT: D  203 ASN cc_start: 0.4112 (OUTLIER) cc_final: 0.3350 (m-40)
REVERT: D  311 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6500 (tt0)
REVERT: D  354 MET cc_start: 0.3724 (ppp) cc_final: 0.2705 (ptt)
REVERT: D  384 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7087 (ptp-170)
REVERT: D  647 ASP cc_start: 0.6951 (m-30) cc_final: 0.6706 (m-30)
REVERT: D  669 TYR cc_start: 0.5915 (m-10) cc_final: 0.5588 (m-10)
REVERT: D  979 LEU cc_start: 0.6387 (OUTLIER) cc_final: 0.6107 (mp)
  outliers start: 42
  outliers final: 21
  residues processed: 159
  average time/residue: 0.5635
  time to fit residues: 101.8754
Evaluate side-chains
  151 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 124
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  384 ARG
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  569 MET
Chi-restraints excluded: chain A residue  681 MET
Chi-restraints excluded: chain A residue  760 PHE
Chi-restraints excluded: chain A residue  810 ASN
Chi-restraints excluded: chain A residue  944 ASP
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  311 GLN
Chi-restraints excluded: chain D residue  314 ILE
Chi-restraints excluded: chain D residue  324 GLU
Chi-restraints excluded: chain D residue  384 ARG
Chi-restraints excluded: chain D residue  388 VAL
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  681 MET
Chi-restraints excluded: chain D residue  731 HIS
Chi-restraints excluded: chain D residue  760 PHE
Chi-restraints excluded: chain D residue  764 HIS
Chi-restraints excluded: chain D residue  979 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 184 optimal weight:    0.6980
   chunk 81 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 183 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0970
   chunk 195 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 102 optimal weight:    6.9990
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 764 HIS
D 203 ASN
** D 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5358 r_free = 0.5358 target = 0.256022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.5275 r_free = 0.5275 target = 0.244008 restraints weight = 20389.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.5280 rms_B_bonded: 0.30
r_work: 0.5139 rms_B_bonded: 0.74 restraints_weight: 0.5000
r_work: 0.5092 rms_B_bonded: 1.50 restraints_weight: 0.2500
r_work: 0.4991 rms_B_bonded: 3.67 restraints_weight: 0.1250
r_work (final): 0.4991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5818
moved from start:          0.3363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  19938  Z= 0.154
  Angle     :  0.596  11.352  27872  Z= 0.333
  Chirality :  0.038   0.192   3096
  Planarity :  0.004   0.044   2804
  Dihedral  : 24.891 125.611   4350
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 20.84 %
    Favored  : 77.16 %
  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:  1.23 (0.20), residues: 1780
  helix:  1.50 (0.15), residues: 1178
  sheet: -0.15 (0.86), residues: 36
  loop : -0.52 (0.27), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  44 
 TYR   0.035   0.002   TYR A 141 
 PHE   0.022   0.002   PHE D 941 
 TRP   0.024   0.001   TRP A 102 
 HIS   0.016   0.001   HIS A 748 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (19938)
  covalent geometry    : angle       0.59625 (27872)
  hydrogen bonds       : bond        0.04300 ( 1127)
  hydrogen bonds       : angle       3.74487 ( 3080)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 130
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.2982 (ptm) cc_final: 0.2213 (ttp)
REVERT: A  388 VAL cc_start: 0.7520 (OUTLIER) cc_final: 0.7297 (p)
REVERT: D  203 ASN cc_start: 0.3881 (OUTLIER) cc_final: 0.3279 (m-40)
REVERT: D  311 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6379 (tt0)
REVERT: D  354 MET cc_start: 0.3423 (ppp) cc_final: 0.2617 (ptt)
REVERT: D  647 ASP cc_start: 0.6848 (m-30) cc_final: 0.6625 (m-30)
REVERT: D  979 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5994 (mp)
  outliers start: 31
  outliers final: 17
  residues processed: 155
  average time/residue: 0.5655
  time to fit residues: 99.9710
Evaluate side-chains
  144 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain A residue  384 ARG
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  681 MET
Chi-restraints excluded: chain A residue  810 ASN
Chi-restraints excluded: chain A residue  944 ASP
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  311 GLN
Chi-restraints excluded: chain D residue  314 ILE
Chi-restraints excluded: chain D residue  324 GLU
Chi-restraints excluded: chain D residue  388 VAL
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  731 HIS
Chi-restraints excluded: chain D residue  760 PHE
Chi-restraints excluded: chain D residue  764 HIS
Chi-restraints excluded: chain D residue  979 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 100 optimal weight:    9.9990
   chunk 78 optimal weight:    7.9990
   chunk 36 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0870
   chunk 159 optimal weight:    0.5980
   chunk 0 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 134 optimal weight:    6.9990
   chunk 4 optimal weight:   20.0000
   chunk 8 optimal weight:    5.9990
   chunk 190 optimal weight:    6.9990
   overall best weight:    2.9364

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

Flipped N/Q/H residues before XYZ refinement:
A 664 GLN
A 764 HIS
** D  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 203 ASN
D 311 GLN
** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5302 r_free = 0.5302 target = 0.250443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5221 r_free = 0.5221 target = 0.238844 restraints weight = 20437.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.5230 rms_B_bonded: 0.27
r_work: 0.5062 rms_B_bonded: 0.65 restraints_weight: 0.5000
r_work: 0.5016 rms_B_bonded: 1.36 restraints_weight: 0.2500
r_work: 0.4960 rms_B_bonded: 2.47 restraints_weight: 0.1250
r_work (final): 0.4960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5944
moved from start:          0.3730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.083  19938  Z= 0.334
  Angle     :  0.773  11.207  27872  Z= 0.421
  Chirality :  0.047   0.235   3096
  Planarity :  0.005   0.061   2804
  Dihedral  : 24.916 122.386   4350
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 20.90 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.29 (0.19), residues: 1780
  helix:  0.75 (0.14), residues: 1184
  sheet:  0.94 (0.77), residues: 20
  loop : -0.87 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 635 
 TYR   0.031   0.003   TYR A 863 
 PHE   0.034   0.003   PHE A 128 
 TRP   0.022   0.002   TRP A 102 
 HIS   0.015   0.002   HIS A 748 

Details of bonding type rmsd
  covalent geometry    : bond        0.00764 (19938)
  covalent geometry    : angle       0.77346 (27872)
  hydrogen bonds       : bond        0.07570 ( 1127)
  hydrogen bonds       : angle       4.21331 ( 3080)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 130
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.3118 (ptm) cc_final: 0.2318 (ttp)
REVERT: A  760 PHE cc_start: 0.5646 (OUTLIER) cc_final: 0.4576 (t80)
REVERT: D  354 MET cc_start: 0.3608 (ppp) cc_final: 0.2815 (ptt)
REVERT: D  647 ASP cc_start: 0.6803 (m-30) cc_final: 0.6564 (m-30)
REVERT: D  832 MET cc_start: 0.5457 (OUTLIER) cc_final: 0.5240 (ttm)
  outliers start: 36
  outliers final: 21
  residues processed: 155
  average time/residue: 0.5538
  time to fit residues: 98.5179
Evaluate side-chains
  147 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  261 GLU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  384 ARG
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  569 MET
Chi-restraints excluded: chain A residue  681 MET
Chi-restraints excluded: chain A residue  760 PHE
Chi-restraints excluded: chain A residue  810 ASN
Chi-restraints excluded: chain A residue  944 ASP
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  314 ILE
Chi-restraints excluded: chain D residue  324 GLU
Chi-restraints excluded: chain D residue  335 THR
Chi-restraints excluded: chain D residue  388 VAL
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  681 MET
Chi-restraints excluded: chain D residue  760 PHE
Chi-restraints excluded: chain D residue  764 HIS
Chi-restraints excluded: chain D residue  832 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 27 optimal weight:    0.5980
   chunk 187 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   chunk 179 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 116 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 496 ASN
** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 764 HIS
** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5353 r_free = 0.5353 target = 0.255679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.5266 r_free = 0.5266 target = 0.243162 restraints weight = 20648.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.5272 rms_B_bonded: 0.31
r_work: 0.5131 rms_B_bonded: 0.81 restraints_weight: 0.5000
r_work: 0.5080 rms_B_bonded: 1.66 restraints_weight: 0.2500
r_work: 0.4930 rms_B_bonded: 4.95 restraints_weight: 0.1250
r_work (final): 0.4930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5921
moved from start:          0.3614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  19938  Z= 0.164
  Angle     :  0.631  12.415  27872  Z= 0.349
  Chirality :  0.039   0.177   3096
  Planarity :  0.004   0.049   2804
  Dihedral  : 24.893 127.675   4350
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 21.61 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  1.05 (0.20), residues: 1780
  helix:  1.34 (0.15), residues: 1172
  sheet:  1.27 (0.81), residues: 20
  loop : -0.54 (0.27), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  44 
 TYR   0.024   0.002   TYR A 863 
 PHE   0.032   0.002   PHE A 128 
 TRP   0.024   0.002   TRP A 102 
 HIS   0.028   0.002   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (19938)
  covalent geometry    : angle       0.63099 (27872)
  hydrogen bonds       : bond        0.04454 ( 1127)
  hydrogen bonds       : angle       3.85847 ( 3080)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6564.22 seconds
wall clock time: 112 minutes 35.41 seconds (6755.41 seconds total)