Starting phenix.real_space_refine
on Sat Aug 23 17:42:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zy5_11550/08_2025/6zy5_11550.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zy5_11550/08_2025/6zy5_11550.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zy5_11550/08_2025/6zy5_11550.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zy5_11550/08_2025/6zy5_11550.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zy5_11550/08_2025/6zy5_11550.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zy5_11550/08_2025/6zy5_11550.cif"
  }
  resolution = 3.6
  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=   0.005 sd=   0.097
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      56      5.49       5
     S      52      5.16       5
     C    8418      2.51       5
     N    2312      2.21       5
     O    2666      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13504
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 6101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 760, 6101
          Classifications: {'peptide': 760}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 34, 'TRANS': 725}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "D"
      Number of atoms: 337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 337
          Classifications: {'DNA': 17}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 16}
    Chain: "E"
      Number of atoms: 272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 272
          Classifications: {'DNA': 13}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 12}
    Chain: "F"
      Number of atoms: 337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 337
          Classifications: {'DNA': 17}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 16}
    Chain: "C"
      Number of atoms: 272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 272
          Classifications: {'DNA': 13}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 12}
    Chain: "A"
      Number of atoms: 6101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 760, 6101
          Classifications: {'peptide': 760}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 34, 'TRANS': 725}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "D"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 42
          Unusual residues: {'EVP': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 42
          Unusual residues: {'EVP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.72, per 1000 atoms: 0.20
  Number of scatterers: 13504
  At special positions: 0
  Unit cell: (103.983, 116.039, 119.053, 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      52     16.00
     P      56     15.00
     O    2666      8.00
     N    2312      7.00
     C    8418      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: 0.98
  Conformation dependent library (CDL) restraints added in 409.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2848

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 14 sheets defined
      52.2% alpha, 6.4% beta
      18 base pairs and 36 stacking pairs defined.
    Time for finding SS restraints: 1.43
  Creating SS restraints...
    Processing helix  chain 'B' and resid 463 through 477
      removed outlier: 3.890A  pdb=" N   THR B 467 " --> pdb=" O   ASP B 463 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU B 468 " --> pdb=" O   SER B 464 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLY B 474 " --> pdb=" O   VAL B 470 " (cutoff:3.500A)
      removed outlier: 5.206A  pdb=" N   VAL B 475 " --> pdb=" O   SER B 471 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   VAL B 476 " --> pdb=" O   GLY B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 504
    Processing helix  chain 'B' and resid 504 through 515
      removed outlier: 4.018A  pdb=" N   ASN B 508 " --> pdb=" O   ASN B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 524 through 531
      removed outlier: 3.587A  pdb=" N   LEU B 528 " --> pdb=" O   ASP B 524 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU B 531 " --> pdb=" O   SER B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 561
      removed outlier: 3.507A  pdb=" N   SER B 547 " --> pdb=" O   ASP B 543 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ASN B 560 " --> pdb=" O   PHE B 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 562 through 567
      removed outlier: 3.576A  pdb=" N   ARG B 566 " --> pdb=" O   SER B 563 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   HIS B 567 " --> pdb=" O   LEU B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 602
    Processing helix  chain 'B' and resid 615 through 619
    Processing helix  chain 'B' and resid 620 through 630
    Processing helix  chain 'B' and resid 630 through 635
      removed outlier: 3.678A  pdb=" N   HIS B 634 " --> pdb=" O   ASP B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 643 through 653
      removed outlier: 3.758A  pdb=" N   ALA B 647 " --> pdb=" O   PRO B 643 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 657 through 679
      removed outlier: 3.595A  pdb=" N   PHE B 668 " --> pdb=" O   TRP B 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 694 through 702
    Processing helix  chain 'B' and resid 702 through 714
    Processing helix  chain 'B' and resid 723 through 736
      removed outlier: 3.547A  pdb=" N   VAL B 729 " --> pdb=" O   GLY B 725 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ARG B 736 " --> pdb=" O   THR B 732 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 744 through 755
    Processing helix  chain 'B' and resid 760 through 771
      removed outlier: 3.775A  pdb=" N   MET B 766 " --> pdb=" O   MET B 762 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   THR B 767 " --> pdb=" O   SER B 763 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 813 through 818
    Processing helix  chain 'B' and resid 819 through 823
      removed outlier: 4.068A  pdb=" N   ASP B 823 " --> pdb=" O   PRO B 820 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 830 through 834
    Processing helix  chain 'B' and resid 847 through 852
    Processing helix  chain 'B' and resid 868 through 882
      removed outlier: 3.726A  pdb=" N   ASP B 881 " --> pdb=" O   ARG B 877 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLY B 882 " --> pdb=" O   ARG B 878 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 931 through 945
      removed outlier: 4.589A  pdb=" N   GLU B 941 " --> pdb=" O   GLU B 937 " (cutoff:3.500A)
      Proline residue:  B 942  - end of helix
      removed outlier: 3.778A  pdb=" N   ASN B 945 " --> pdb=" O   GLU B 941 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 973 through 984
    Processing helix  chain 'B' and resid 984 through 989
    Processing helix  chain 'B' and resid 1014 through 1028
      removed outlier: 3.649A  pdb=" N   ILE B1018 " --> pdb=" O   THR B1014 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1029 through 1061
      removed outlier: 4.800A  pdb=" N   GLY B1039 " --> pdb=" O   GLU B1035 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   MET B1040 " --> pdb=" O   TRP B1036 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   GLY B1042 " --> pdb=" O   LEU B1038 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1069 through 1080
      removed outlier: 3.686A  pdb=" N   ARG B1080 " --> pdb=" O   VAL B1076 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1085 through 1096
    Processing helix  chain 'B' and resid 1132 through 1136
    Processing helix  chain 'B' and resid 1137 through 1161
      removed outlier: 3.998A  pdb=" N   GLU B1143 " --> pdb=" O   GLU B1139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1165 through 1193
      removed outlier: 3.696A  pdb=" N   ALA B1180 " --> pdb=" O   GLU B1176 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU B1189 " --> pdb=" O   GLU B1185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 477
      removed outlier: 3.890A  pdb=" N   THR A 467 " --> pdb=" O   ASP A 463 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU A 468 " --> pdb=" O   SER A 464 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY A 474 " --> pdb=" O   VAL A 470 " (cutoff:3.500A)
      removed outlier: 5.204A  pdb=" N   VAL A 475 " --> pdb=" O   SER A 471 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   VAL A 476 " --> pdb=" O   GLY A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 504
    Processing helix  chain 'A' and resid 504 through 515
      removed outlier: 4.019A  pdb=" N   ASN A 508 " --> pdb=" O   ASN A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 531
      removed outlier: 3.588A  pdb=" N   LEU A 528 " --> pdb=" O   ASP A 524 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LEU A 531 " --> pdb=" O   SER A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 561
      removed outlier: 3.508A  pdb=" N   SER A 547 " --> pdb=" O   ASP A 543 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ASN A 560 " --> pdb=" O   PHE A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 567
      removed outlier: 3.576A  pdb=" N   ARG A 566 " --> pdb=" O   SER A 563 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   HIS A 567 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 615 through 619
    Processing helix  chain 'A' and resid 620 through 630
    Processing helix  chain 'A' and resid 630 through 635
      removed outlier: 3.678A  pdb=" N   HIS A 634 " --> pdb=" O   ASP A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 653
      removed outlier: 3.759A  pdb=" N   ALA A 647 " --> pdb=" O   PRO A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 657 through 679
      removed outlier: 3.596A  pdb=" N   PHE A 668 " --> pdb=" O   TRP A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 694 through 702
    Processing helix  chain 'A' and resid 702 through 714
    Processing helix  chain 'A' and resid 723 through 736
      removed outlier: 3.547A  pdb=" N   VAL A 729 " --> pdb=" O   GLY A 725 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ARG A 736 " --> pdb=" O   THR A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 755
    Processing helix  chain 'A' and resid 760 through 771
      removed outlier: 3.773A  pdb=" N   MET A 766 " --> pdb=" O   MET A 762 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   THR A 767 " --> pdb=" O   SER A 763 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 818
    Processing helix  chain 'A' and resid 819 through 823
      removed outlier: 4.070A  pdb=" N   ASP A 823 " --> pdb=" O   PRO A 820 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 834
    Processing helix  chain 'A' and resid 847 through 852
    Processing helix  chain 'A' and resid 868 through 882
      removed outlier: 3.726A  pdb=" N   ASP A 881 " --> pdb=" O   ARG A 877 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLY A 882 " --> pdb=" O   ARG A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 931 through 945
      removed outlier: 4.587A  pdb=" N   GLU A 941 " --> pdb=" O   GLU A 937 " (cutoff:3.500A)
      Proline residue:  A 942  - end of helix
      removed outlier: 3.779A  pdb=" N   ASN A 945 " --> pdb=" O   GLU A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 984
    Processing helix  chain 'A' and resid 984 through 989
    Processing helix  chain 'A' and resid 1014 through 1028
      removed outlier: 3.649A  pdb=" N   ILE A1018 " --> pdb=" O   THR A1014 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1029 through 1061
      removed outlier: 4.798A  pdb=" N   GLY A1039 " --> pdb=" O   GLU A1035 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   MET A1040 " --> pdb=" O   TRP A1036 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   GLY A1042 " --> pdb=" O   LEU A1038 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1080
      removed outlier: 3.686A  pdb=" N   ARG A1080 " --> pdb=" O   VAL A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1096
    Processing helix  chain 'A' and resid 1132 through 1136
    Processing helix  chain 'A' and resid 1137 through 1161
      removed outlier: 3.998A  pdb=" N   GLU A1143 " --> pdb=" O   GLU A1139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1165 through 1193
      removed outlier: 3.696A  pdb=" N   ALA A1180 " --> pdb=" O   GLU A1176 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLU A1189 " --> pdb=" O   GLU A1185 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 483 through 485
      removed outlier: 6.594A  pdb=" N   ILE B 458 " --> pdb=" O   PHE B 484 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   LEU B 459 " --> pdb=" O   MET B 539 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 588 through 589
      removed outlier: 3.551A  pdb=" N   VAL B 578 " --> pdb=" O   PHE B 589 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 742 through 743
    Processing sheet with id=AA4, first strand: chain 'B' and resid 853 through 856
    Processing sheet with id=AA5, first strand: chain 'B' and resid 898 through 901
    Processing sheet with id=AA6, first strand: chain 'B' and resid 956 through 959
      removed outlier: 6.340A  pdb=" N   GLU B 912 " --> pdb=" O   SER B 924 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LYS B1203 " --> pdb=" O   ILE B 915 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1001 through 1002
      removed outlier: 3.622A  pdb=" N   LEU B1002 " --> pdb=" O   LYS B1010 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 483 through 485
      removed outlier: 6.594A  pdb=" N   ILE A 458 " --> pdb=" O   PHE A 484 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   LEU A 459 " --> pdb=" O   MET A 539 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 589
      removed outlier: 3.551A  pdb=" N   VAL A 578 " --> pdb=" O   PHE A 589 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 742 through 743
    Processing sheet with id=AB2, first strand: chain 'A' and resid 853 through 856
    Processing sheet with id=AB3, first strand: chain 'A' and resid 898 through 901
    Processing sheet with id=AB4, first strand: chain 'A' and resid 956 through 959
      removed outlier: 6.342A  pdb=" N   GLU A 912 " --> pdb=" O   SER A 924 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   LYS A1203 " --> pdb=" O   ILE A 915 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1001 through 1002
      removed outlier: 3.621A  pdb=" N   LEU A1002 " --> pdb=" O   LYS A1010 " (cutoff:3.500A)

    548 hydrogen bonds defined for protein.
    1542 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      43 hydrogen bonds
      86 hydrogen bond angles
      0 basepair planarities
      18 basepair parallelities
      36 stacking parallelities
  Total time for adding SS restraints: 2.10

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2331
        1.32 -     1.44: 3733
        1.44 -     1.57: 7640
        1.57 -     1.69: 112
        1.69 -     1.82: 92
  Bond restraints: 13908
  Sorted by residual:
  bond pdb=" C   LYS B1071 "
       pdb=" O   LYS B1071 "
    ideal  model  delta    sigma   weight residual
    1.237  1.287 -0.050 1.16e-02 7.43e+03 1.89e+01
  bond pdb=" C   LYS A1071 "
       pdb=" O   LYS A1071 "
    ideal  model  delta    sigma   weight residual
    1.237  1.287 -0.050 1.16e-02 7.43e+03 1.88e+01
  bond pdb=" C   ILE B1074 "
       pdb=" O   ILE B1074 "
    ideal  model  delta    sigma   weight residual
    1.237  1.288 -0.051 1.17e-02 7.31e+03 1.87e+01
  bond pdb=" C   ILE A1074 "
       pdb=" O   ILE A1074 "
    ideal  model  delta    sigma   weight residual
    1.237  1.287 -0.050 1.17e-02 7.31e+03 1.80e+01
  bond pdb=" CA  SER B 861 "
       pdb=" CB  SER B 861 "
    ideal  model  delta    sigma   weight residual
    1.534  1.469  0.066 1.77e-02 3.19e+03 1.38e+01
  ... (remaining 13903 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 15357
        1.53 -     3.05: 3411
        3.05 -     4.58: 230
        4.58 -     6.10: 30
        6.10 -     7.63: 2
  Bond angle restraints: 19030
  Sorted by residual:
  angle pdb=" CA  SER A 861 "
        pdb=" C   SER A 861 "
        pdb=" O   SER A 861 "
      ideal   model   delta    sigma   weight residual
     121.51  116.15    5.36 1.12e+00 7.97e-01 2.29e+01
  angle pdb=" CA  SER B 861 "
        pdb=" C   SER B 861 "
        pdb=" O   SER B 861 "
      ideal   model   delta    sigma   weight residual
     121.51  116.29    5.22 1.12e+00 7.97e-01 2.17e+01
  angle pdb=" N   LEU B1166 "
        pdb=" CA  LEU B1166 "
        pdb=" C   LEU B1166 "
      ideal   model   delta    sigma   weight residual
     112.23  106.62    5.61 1.26e+00 6.30e-01 1.98e+01
  angle pdb=" N   LEU A1166 "
        pdb=" CA  LEU A1166 "
        pdb=" C   LEU A1166 "
      ideal   model   delta    sigma   weight residual
     112.23  106.63    5.60 1.26e+00 6.30e-01 1.98e+01
  angle pdb=" N   ILE B1065 "
        pdb=" CA  ILE B1065 "
        pdb=" C   ILE B1065 "
      ideal   model   delta    sigma   weight residual
     112.43  108.58    3.85 9.20e-01 1.18e+00 1.75e+01
  ... (remaining 19025 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.12: 8028
       28.12 -    56.24: 307
       56.24 -    84.36: 45
       84.36 -   112.48: 2
      112.48 -   140.60: 2
  Dihedral angle restraints: 8384
    sinusoidal: 3964
      harmonic: 4420
  Sorted by residual:
  dihedral pdb=" C4'  DC E   9 "
           pdb=" C3'  DC E   9 "
           pdb=" O3'  DC E   9 "
           pdb=" P    DG E  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   79.40  140.60     1      3.50e+01 8.16e-04 1.39e+01
  dihedral pdb=" C4'  DC C   9 "
           pdb=" C3'  DC C   9 "
           pdb=" O3'  DC C   9 "
           pdb=" P    DG C  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   79.49  140.51     1      3.50e+01 8.16e-04 1.39e+01
  dihedral pdb=" C   TYR A 830 "
           pdb=" N   TYR A 830 "
           pdb=" CA  TYR A 830 "
           pdb=" CB  TYR A 830 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.77    9.17     0      2.50e+00 1.60e-01 1.34e+01
  ... (remaining 8381 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1060
       0.058 -    0.115: 634
       0.115 -    0.173: 308
       0.173 -    0.230: 82
       0.230 -    0.288: 10
  Chirality restraints: 2094
  Sorted by residual:
  chirality pdb=" CA  ILE B 915 "
            pdb=" N   ILE B 915 "
            pdb=" C   ILE B 915 "
            pdb=" CB  ILE B 915 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.72   -0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" CA  ILE A 915 "
            pdb=" N   ILE A 915 "
            pdb=" C   ILE A 915 "
            pdb=" CB  ILE A 915 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.72   -0.29 2.00e-01 2.50e+01 2.04e+00
  chirality pdb=" CA  ILE A 864 "
            pdb=" N   ILE A 864 "
            pdb=" C   ILE A 864 "
            pdb=" CB  ILE A 864 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.56e+00
  ... (remaining 2091 not shown)

  Planarity restraints: 2220
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS B 824 "   -0.011 2.00e-02 2.50e+03   2.32e-02 5.37e+00
        pdb=" C   HIS B 824 "    0.040 2.00e-02 2.50e+03
        pdb=" O   HIS B 824 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   THR B 825 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 824 "   -0.011 2.00e-02 2.50e+03   2.31e-02 5.33e+00
        pdb=" C   HIS A 824 "    0.040 2.00e-02 2.50e+03
        pdb=" O   HIS A 824 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   THR A 825 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 936 "   -0.011 2.00e-02 2.50e+03   2.29e-02 5.25e+00
        pdb=" C   LYS A 936 "    0.040 2.00e-02 2.50e+03
        pdb=" O   LYS A 936 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLU A 937 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 2217 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1615
        2.76 -     3.29: 13178
        3.29 -     3.83: 20913
        3.83 -     4.36: 25193
        4.36 -     4.90: 41052
  Nonbonded interactions: 101951
  Sorted by model distance:
  nonbonded pdb=" O6   DG E  13 "
            pdb=" O13 EVP F 101 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OE1 GLN B1094 "
            pdb=" NE2 GLN B1095 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" OE1 GLN A1094 "
            pdb=" NE2 GLN A1095 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" NH2 ARG A 870 "
            pdb=" OE1 GLU A1182 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" NH2 ARG B 870 "
            pdb=" OE1 GLU B1182 "
     model   vdw
     2.349 3.120
  ... (remaining 101946 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.940
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.330
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
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      :  0.011   0.066  13908  Z= 0.776
  Angle     :  1.165   7.628  19030  Z= 0.866
  Chirality :  0.086   0.288   2094
  Planarity :  0.007   0.039   2220
  Dihedral  : 13.851 140.604   5536
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.90 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.64 (0.21), residues: 1512
  helix:  1.50 (0.19), residues: 678
  sheet: -1.37 (0.37), residues: 198
  loop : -2.35 (0.23), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 804 
 TYR   0.022   0.002   TYR B 830 
 PHE   0.010   0.002   PHE A 818 
 TRP   0.011   0.003   TRP B1090 
 HIS   0.004   0.001   HIS B 986 

Details of bonding type rmsd
  covalent geometry    : bond        0.01086 (13908)
  covalent geometry    : angle       1.16511 (19030)
  hydrogen bonds       : bond        0.18509 (  591)
  hydrogen bonds       : angle       5.96383 ( 1628)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  473 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 471
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  498 HIS cc_start: 0.5973 (t70) cc_final: 0.5327 (t-170)
REVERT: B  530 THR cc_start: 0.8648 (m) cc_final: 0.8420 (p)
REVERT: B  657 GLN cc_start: 0.7537 (mt0) cc_final: 0.7252 (mm-40)
REVERT: B  714 SER cc_start: 0.8491 (m) cc_final: 0.8194 (t)
REVERT: B  766 MET cc_start: 0.7498 (ttm) cc_final: 0.7254 (ttm)
REVERT: B  774 ASN cc_start: 0.8606 (p0) cc_final: 0.8332 (p0)
REVERT: B  805 TYR cc_start: 0.7935 (m-10) cc_final: 0.7621 (m-10)
REVERT: B  856 ILE cc_start: 0.9163 (mt) cc_final: 0.8945 (mt)
REVERT: B  916 LEU cc_start: 0.8902 (mt) cc_final: 0.7892 (tt)
REVERT: B 1053 ARG cc_start: 0.6470 (mmm160) cc_final: 0.6143 (ttp80)
REVERT: A  498 HIS cc_start: 0.5993 (t70) cc_final: 0.5645 (t-170)
REVERT: A  529 LYS cc_start: 0.7905 (tttt) cc_final: 0.7598 (mtpt)
REVERT: A  530 THR cc_start: 0.8655 (m) cc_final: 0.8421 (p)
REVERT: A  657 GLN cc_start: 0.7518 (mt0) cc_final: 0.7242 (mm-40)
REVERT: A  714 SER cc_start: 0.8492 (m) cc_final: 0.8146 (t)
REVERT: A  766 MET cc_start: 0.7446 (ttm) cc_final: 0.7180 (ttm)
REVERT: A  774 ASN cc_start: 0.8616 (p0) cc_final: 0.8343 (p0)
REVERT: A  805 TYR cc_start: 0.7925 (m-10) cc_final: 0.7614 (m-10)
REVERT: A  856 ILE cc_start: 0.9244 (mt) cc_final: 0.9040 (mt)
REVERT: A  916 LEU cc_start: 0.8896 (mt) cc_final: 0.7880 (tt)
REVERT: A 1053 ARG cc_start: 0.6472 (mmm160) cc_final: 0.6138 (ttp80)
  outliers start: 2
  outliers final: 2
  residues processed: 473
  average time/residue: 0.1219
  time to fit residues: 78.5098
Evaluate side-chains
  223 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 221
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 1078 ILE
Chi-restraints excluded: chain A residue 1078 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 498 HIS
B 634 HIS
** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 833 ASN
A 634 HIS
** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 833 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.150546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.128899 restraints weight = 20874.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.132267 restraints weight = 12094.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.134602 restraints weight = 8247.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.136151 restraints weight = 6275.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.137336 restraints weight = 5171.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13908  Z= 0.152
  Angle     :  0.563   5.927  19030  Z= 0.300
  Chirality :  0.040   0.169   2094
  Planarity :  0.004   0.037   2220
  Dihedral  : 17.712 136.177   2424
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 11.37 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.22), residues: 1512
  helix:  1.99 (0.20), residues: 678
  sheet: -1.33 (0.39), residues: 196
  loop : -2.12 (0.24), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B1146 
 TYR   0.016   0.001   TYR A 957 
 PHE   0.014   0.001   PHE B 807 
 TRP   0.015   0.002   TRP A 664 
 HIS   0.005   0.001   HIS B 605 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (13908)
  covalent geometry    : angle       0.56290 (19030)
  hydrogen bonds       : bond        0.04072 (  591)
  hydrogen bonds       : angle       4.00386 ( 1628)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 214
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  503 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7648 (mm-30)
REVERT: B  712 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7365 (mt-10)
REVERT: B  737 ASN cc_start: 0.7832 (t0) cc_final: 0.7558 (t0)
REVERT: B  774 ASN cc_start: 0.8579 (p0) cc_final: 0.8288 (p0)
REVERT: B 1053 ARG cc_start: 0.7066 (mmm160) cc_final: 0.6388 (ttm170)
REVERT: B 1153 GLN cc_start: 0.6589 (mm-40) cc_final: 0.6225 (mt0)
REVERT: A  503 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7623 (mm-30)
REVERT: A  529 LYS cc_start: 0.7556 (tttt) cc_final: 0.7282 (mtpt)
REVERT: A  712 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7339 (mt-10)
REVERT: A  737 ASN cc_start: 0.7848 (t0) cc_final: 0.7645 (t0)
REVERT: A  774 ASN cc_start: 0.8584 (p0) cc_final: 0.8306 (p0)
REVERT: A 1053 ARG cc_start: 0.7055 (mmm160) cc_final: 0.6387 (ttm170)
REVERT: A 1153 GLN cc_start: 0.6584 (mm-40) cc_final: 0.6229 (mt0)
  outliers start: 30
  outliers final: 20
  residues processed: 242
  average time/residue: 0.1029
  time to fit residues: 35.7225
Evaluate side-chains
  175 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  541 ASP
Chi-restraints excluded: chain B residue  768 ILE
Chi-restraints excluded: chain B residue  821 LYS
Chi-restraints excluded: chain B residue  898 THR
Chi-restraints excluded: chain B residue  955 THR
Chi-restraints excluded: chain B residue 1044 GLU
Chi-restraints excluded: chain B residue 1056 LEU
Chi-restraints excluded: chain B residue 1145 CYS
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  541 ASP
Chi-restraints excluded: chain A residue  768 ILE
Chi-restraints excluded: chain A residue  821 LYS
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  955 THR
Chi-restraints excluded: chain A residue 1044 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1145 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 105 optimal weight:    5.9990
   chunk 131 optimal weight:    7.9990
   chunk 151 optimal weight:    0.9980
   chunk 132 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 145 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 100 optimal weight:    0.5980
   chunk 116 optimal weight:    4.9990
   overall best weight:    1.4782

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

Flipped N/Q/H residues before XYZ refinement:
B 508 ASN
B 559 HIS
** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 508 ASN
A 559 HIS
** A 746 GLN ** 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 = 0.3776 r_free = 0.3776 target = 0.135691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.111073 restraints weight = 23664.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.114542 restraints weight = 12889.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.116908 restraints weight = 8582.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.118536 restraints weight = 6520.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.119691 restraints weight = 5377.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.5069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  13908  Z= 0.212
  Angle     :  0.626   5.278  19030  Z= 0.335
  Chirality :  0.044   0.161   2094
  Planarity :  0.004   0.034   2220
  Dihedral  : 17.957 134.310   2420
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 13.40 %
    Favored  : 83.51 %
  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 aren not related in a simple way.
  whole: -0.27 (0.22), residues: 1512
  helix:  1.68 (0.20), residues: 700
  sheet: -1.49 (0.38), residues: 216
  loop : -2.00 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 713 
 TYR   0.023   0.002   TYR B1029 
 PHE   0.014   0.002   PHE A 790 
 TRP   0.018   0.002   TRP B1090 
 HIS   0.007   0.001   HIS B 605 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 (13908)
  covalent geometry    : angle       0.62608 (19030)
  hydrogen bonds       : bond        0.04767 (  591)
  hydrogen bonds       : angle       4.11723 ( 1628)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 162
  time to evaluate  : 0.390 
Fit side-chains
REVERT: B  568 ARG cc_start: 0.7959 (mtp85) cc_final: 0.7630 (mtp180)
REVERT: B  751 VAL cc_start: 0.8877 (t) cc_final: 0.8544 (t)
REVERT: B  755 SER cc_start: 0.9007 (OUTLIER) cc_final: 0.8459 (t)
REVERT: B  831 ASP cc_start: 0.7195 (t0) cc_final: 0.6965 (t0)
REVERT: B  922 GLU cc_start: 0.7188 (tt0) cc_final: 0.6949 (pt0)
REVERT: B 1153 GLN cc_start: 0.6572 (mm-40) cc_final: 0.6161 (mt0)
REVERT: A  529 LYS cc_start: 0.8000 (tttt) cc_final: 0.7482 (mtpt)
REVERT: A  568 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7650 (mtp180)
REVERT: A  751 VAL cc_start: 0.8739 (t) cc_final: 0.8405 (t)
REVERT: A  755 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8483 (t)
REVERT: A  883 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7614 (mt-10)
REVERT: A  922 GLU cc_start: 0.7222 (tt0) cc_final: 0.6918 (pt0)
REVERT: A 1153 GLN cc_start: 0.6560 (mm-40) cc_final: 0.6158 (mt0)
  outliers start: 41
  outliers final: 17
  residues processed: 194
  average time/residue: 0.0922
  time to fit residues: 26.7173
Evaluate side-chains
  143 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 CYS
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  541 ASP
Chi-restraints excluded: chain B residue  755 SER
Chi-restraints excluded: chain B residue  768 ILE
Chi-restraints excluded: chain B residue  920 THR
Chi-restraints excluded: chain B residue  940 LEU
Chi-restraints excluded: chain B residue 1056 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  541 ASP
Chi-restraints excluded: chain A residue  755 SER
Chi-restraints excluded: chain A residue  768 ILE
Chi-restraints excluded: chain A residue  920 THR
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue 1056 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 46 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 134 optimal weight:    7.9990
   chunk 128 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.137178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.112692 restraints weight = 23316.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.116204 restraints weight = 12646.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.118615 restraints weight = 8398.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.120258 restraints weight = 6337.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.121427 restraints weight = 5217.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.5319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  13908  Z= 0.131
  Angle     :  0.512   5.570  19030  Z= 0.274
  Chirality :  0.039   0.150   2094
  Planarity :  0.003   0.030   2220
  Dihedral  : 17.810 134.397   2420
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.91 %
    Favored  : 83.13 %
  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 aren not related in a simple way.
  whole:  0.00 (0.23), residues: 1512
  helix:  1.90 (0.20), residues: 702
  sheet: -1.27 (0.39), residues: 196
  loop : -1.89 (0.25), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 494 
 TYR   0.012   0.001   TYR A 957 
 PHE   0.010   0.001   PHE B 706 
 TRP   0.009   0.001   TRP B 664 
 HIS   0.005   0.001   HIS B 605 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (13908)
  covalent geometry    : angle       0.51207 (19030)
  hydrogen bonds       : bond        0.03537 (  591)
  hydrogen bonds       : angle       3.73194 ( 1628)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 0.490 
Fit side-chains
REVERT: B  751 VAL cc_start: 0.8904 (t) cc_final: 0.8571 (t)
REVERT: B  755 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8304 (t)
REVERT: B  864 ILE cc_start: 0.8363 (mm) cc_final: 0.8142 (mt)
REVERT: B 1030 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.7466 (m-80)
REVERT: B 1153 GLN cc_start: 0.6503 (mm-40) cc_final: 0.6087 (mt0)
REVERT: A  528 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7518 (mp)
REVERT: A  529 LYS cc_start: 0.7718 (tttt) cc_final: 0.7328 (mtpt)
REVERT: A  751 VAL cc_start: 0.8916 (t) cc_final: 0.8580 (t)
REVERT: A  755 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8264 (t)
REVERT: A  827 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7928 (ptmm)
REVERT: A  831 ASP cc_start: 0.7357 (t0) cc_final: 0.7078 (t0)
REVERT: A 1030 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.7455 (m-80)
REVERT: A 1153 GLN cc_start: 0.6506 (mm-40) cc_final: 0.6092 (mt0)
  outliers start: 26
  outliers final: 13
  residues processed: 175
  average time/residue: 0.0947
  time to fit residues: 25.7533
Evaluate side-chains
  150 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 CYS
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  755 SER
Chi-restraints excluded: chain B residue  898 THR
Chi-restraints excluded: chain B residue 1030 TYR
Chi-restraints excluded: chain B residue 1044 GLU
Chi-restraints excluded: chain B residue 1056 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  526 ASP
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  755 SER
Chi-restraints excluded: chain A residue  827 LYS
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1030 TYR
Chi-restraints excluded: chain A residue 1044 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 102 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 127 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 135 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 134 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.137534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.115449 restraints weight = 21185.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.118472 restraints weight = 12491.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.120556 restraints weight = 8678.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.122025 restraints weight = 6754.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.123066 restraints weight = 5640.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.5660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  13908  Z= 0.145
  Angle     :  0.525   7.337  19030  Z= 0.280
  Chirality :  0.039   0.148   2094
  Planarity :  0.004   0.033   2220
  Dihedral  : 17.881 135.824   2420
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.81 %
    Favored  : 81.85 %
  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 aren not related in a simple way.
  whole:  0.15 (0.23), residues: 1512
  helix:  2.02 (0.20), residues: 698
  sheet: -1.14 (0.42), residues: 178
  loop : -1.81 (0.24), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 568 
 TYR   0.011   0.001   TYR B1012 
 PHE   0.010   0.001   PHE B 653 
 TRP   0.009   0.001   TRP B 664 
 HIS   0.006   0.001   HIS B 605 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (13908)
  covalent geometry    : angle       0.52513 (19030)
  hydrogen bonds       : bond        0.03910 (  591)
  hydrogen bonds       : angle       3.78604 ( 1628)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 148
  time to evaluate  : 0.426 
Fit side-chains
REVERT: B  506 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6809 (pm20)
REVERT: B  751 VAL cc_start: 0.9131 (t) cc_final: 0.8781 (t)
REVERT: B  755 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8513 (t)
REVERT: B  864 ILE cc_start: 0.8470 (mm) cc_final: 0.8191 (mt)
REVERT: B 1033 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.6830 (tpp80)
REVERT: B 1153 GLN cc_start: 0.6745 (mm-40) cc_final: 0.6396 (mt0)
REVERT: A  506 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6806 (pm20)
REVERT: A  529 LYS cc_start: 0.7535 (tttt) cc_final: 0.7258 (mtpt)
REVERT: A  669 MET cc_start: 0.8637 (mtp) cc_final: 0.8228 (mtp)
REVERT: A  751 VAL cc_start: 0.9132 (t) cc_final: 0.8782 (t)
REVERT: A  755 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8483 (t)
REVERT: A  827 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8136 (ptmm)
REVERT: A  864 ILE cc_start: 0.8458 (mm) cc_final: 0.8181 (mt)
REVERT: A 1033 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.6818 (tpp80)
REVERT: A 1153 GLN cc_start: 0.6740 (mm-40) cc_final: 0.6412 (mt0)
  outliers start: 31
  outliers final: 18
  residues processed: 172
  average time/residue: 0.0952
  time to fit residues: 23.9139
Evaluate side-chains
  159 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 CYS
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  506 GLU
Chi-restraints excluded: chain B residue  755 SER
Chi-restraints excluded: chain B residue  845 ILE
Chi-restraints excluded: chain B residue  898 THR
Chi-restraints excluded: chain B residue 1033 ARG
Chi-restraints excluded: chain B residue 1044 GLU
Chi-restraints excluded: chain B residue 1056 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  506 GLU
Chi-restraints excluded: chain A residue  526 ASP
Chi-restraints excluded: chain A residue  755 SER
Chi-restraints excluded: chain A residue  825 THR
Chi-restraints excluded: chain A residue  827 LYS
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1033 ARG
Chi-restraints excluded: chain A residue 1044 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1177 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 122 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0170
   chunk 116 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 123 optimal weight:    0.9990
   chunk 105 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.8022

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

Flipped N/Q/H residues before XYZ refinement:
** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.137730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.115131 restraints weight = 21408.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.118246 restraints weight = 12570.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.120402 restraints weight = 8698.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.121883 restraints weight = 6769.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.122919 restraints weight = 5659.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.5829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  13908  Z= 0.130
  Angle     :  0.512   8.339  19030  Z= 0.272
  Chirality :  0.038   0.151   2094
  Planarity :  0.003   0.033   2220
  Dihedral  : 17.847 136.345   2420
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 16.94 %
    Favored  : 81.10 %
  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 aren not related in a simple way.
  whole:  0.34 (0.23), residues: 1512
  helix:  2.21 (0.20), residues: 698
  sheet: -1.07 (0.43), residues: 178
  loop : -1.74 (0.24), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1026 
 TYR   0.009   0.001   TYR A 957 
 PHE   0.009   0.001   PHE B 653 
 TRP   0.009   0.001   TRP A 664 
 HIS   0.005   0.001   HIS B 605 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (13908)
  covalent geometry    : angle       0.51181 (19030)
  hydrogen bonds       : bond        0.03650 (  591)
  hydrogen bonds       : angle       3.69595 ( 1628)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 0.333 
Fit side-chains
REVERT: B  669 MET cc_start: 0.8666 (mtp) cc_final: 0.8268 (mtp)
REVERT: B  751 VAL cc_start: 0.9123 (t) cc_final: 0.8853 (t)
REVERT: B  755 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8419 (t)
REVERT: B 1033 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6874 (tpp80)
REVERT: B 1153 GLN cc_start: 0.6714 (mm-40) cc_final: 0.6347 (mt0)
REVERT: A  529 LYS cc_start: 0.7547 (tttt) cc_final: 0.7258 (mtpt)
REVERT: A  669 MET cc_start: 0.8648 (mtp) cc_final: 0.8198 (mtp)
REVERT: A  751 VAL cc_start: 0.9104 (t) cc_final: 0.8765 (t)
REVERT: A  755 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8445 (t)
REVERT: A  827 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8094 (ptmm)
REVERT: A 1033 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6883 (tpp80)
REVERT: A 1153 GLN cc_start: 0.6721 (mm-40) cc_final: 0.6345 (mt0)
  outliers start: 26
  outliers final: 19
  residues processed: 162
  average time/residue: 0.0891
  time to fit residues: 22.2736
Evaluate side-chains
  157 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 CYS
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  755 SER
Chi-restraints excluded: chain B residue  825 THR
Chi-restraints excluded: chain B residue  845 ILE
Chi-restraints excluded: chain B residue  898 THR
Chi-restraints excluded: chain B residue  913 VAL
Chi-restraints excluded: chain B residue 1033 ARG
Chi-restraints excluded: chain B residue 1044 GLU
Chi-restraints excluded: chain B residue 1056 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  526 ASP
Chi-restraints excluded: chain A residue  755 SER
Chi-restraints excluded: chain A residue  827 LYS
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1033 ARG
Chi-restraints excluded: chain A residue 1044 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1177 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 113 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 146 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 153 optimal weight:    0.0870
   overall best weight:    0.7958

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

Flipped N/Q/H residues before XYZ refinement:
** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 779 ASN
** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.137661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.115012 restraints weight = 21266.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.118148 restraints weight = 12444.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.120336 restraints weight = 8591.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.121842 restraints weight = 6643.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.122734 restraints weight = 5548.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.5985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  13908  Z= 0.128
  Angle     :  0.510   9.353  19030  Z= 0.270
  Chirality :  0.038   0.148   2094
  Planarity :  0.003   0.030   2220
  Dihedral  : 17.862 136.575   2420
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.79 %
    Favored  : 80.65 %
  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 aren not related in a simple way.
  whole:  0.40 (0.23), residues: 1512
  helix:  2.24 (0.20), residues: 698
  sheet: -1.06 (0.43), residues: 178
  loop : -1.69 (0.24), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 478 
 TYR   0.024   0.001   TYR A1127 
 PHE   0.009   0.001   PHE A 653 
 TRP   0.009   0.001   TRP B1167 
 HIS   0.005   0.001   HIS B 605 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (13908)
  covalent geometry    : angle       0.51027 (19030)
  hydrogen bonds       : bond        0.03657 (  591)
  hydrogen bonds       : angle       3.69566 ( 1628)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 139
  time to evaluate  : 0.347 
Fit side-chains
REVERT: B  506 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6751 (pm20)
REVERT: B  669 MET cc_start: 0.8668 (mtp) cc_final: 0.8228 (mtp)
REVERT: B  751 VAL cc_start: 0.9157 (t) cc_final: 0.8888 (t)
REVERT: B  755 SER cc_start: 0.8954 (OUTLIER) cc_final: 0.8477 (t)
REVERT: B 1033 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.6930 (tpp80)
REVERT: B 1153 GLN cc_start: 0.6726 (mm-40) cc_final: 0.6331 (mt0)
REVERT: A  506 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6743 (pm20)
REVERT: A  529 LYS cc_start: 0.7696 (tttt) cc_final: 0.7299 (mtpt)
REVERT: A  669 MET cc_start: 0.8658 (mtp) cc_final: 0.8181 (mtp)
REVERT: A  755 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8478 (t)
REVERT: A  827 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8067 (ptmm)
REVERT: A 1033 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6944 (tpp80)
REVERT: A 1153 GLN cc_start: 0.6710 (mm-40) cc_final: 0.6327 (mt0)
  outliers start: 34
  outliers final: 21
  residues processed: 167
  average time/residue: 0.0946
  time to fit residues: 23.7846
Evaluate side-chains
  160 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 CYS
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  506 GLU
Chi-restraints excluded: chain B residue  703 LEU
Chi-restraints excluded: chain B residue  755 SER
Chi-restraints excluded: chain B residue  825 THR
Chi-restraints excluded: chain B residue  845 ILE
Chi-restraints excluded: chain B residue  898 THR
Chi-restraints excluded: chain B residue  913 VAL
Chi-restraints excluded: chain B residue 1033 ARG
Chi-restraints excluded: chain B residue 1044 GLU
Chi-restraints excluded: chain B residue 1056 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  506 GLU
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  755 SER
Chi-restraints excluded: chain A residue  825 THR
Chi-restraints excluded: chain A residue  827 LYS
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue 1033 ARG
Chi-restraints excluded: chain A residue 1044 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1177 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 128 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 153 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 114 optimal weight:    0.0040
   overall best weight:    1.1396

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

Flipped N/Q/H residues before XYZ refinement:
** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.135744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.113209 restraints weight = 21214.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.116314 restraints weight = 12423.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.118440 restraints weight = 8555.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.119876 restraints weight = 6636.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.120915 restraints weight = 5558.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.6217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13908  Z= 0.162
  Angle     :  0.556   8.479  19030  Z= 0.292
  Chirality :  0.040   0.145   2094
  Planarity :  0.004   0.032   2220
  Dihedral  : 17.988 136.505   2420
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.55 %
    Favored  : 80.12 %
  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 aren not related in a simple way.
  whole:  0.24 (0.23), residues: 1512
  helix:  1.99 (0.20), residues: 714
  sheet: -1.10 (0.42), residues: 178
  loop : -1.73 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 478 
 TYR   0.010   0.001   TYR A1012 
 PHE   0.011   0.001   PHE A 653 
 TRP   0.009   0.001   TRP B 664 
 HIS   0.005   0.001   HIS B 605 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (13908)
  covalent geometry    : angle       0.55575 (19030)
  hydrogen bonds       : bond        0.04133 (  591)
  hydrogen bonds       : angle       3.83469 ( 1628)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 0.371 
Fit side-chains
REVERT: B  506 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6865 (pm20)
REVERT: B  669 MET cc_start: 0.8575 (mtp) cc_final: 0.8123 (mtp)
REVERT: B  755 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8533 (t)
REVERT: B  864 ILE cc_start: 0.8485 (mm) cc_final: 0.8171 (mt)
REVERT: B  976 LYS cc_start: 0.7376 (mttt) cc_final: 0.7162 (mmmm)
REVERT: B 1033 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6899 (tpp80)
REVERT: B 1153 GLN cc_start: 0.6763 (mm-40) cc_final: 0.6368 (mt0)
REVERT: A  506 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6843 (pm20)
REVERT: A  529 LYS cc_start: 0.7551 (tttt) cc_final: 0.7175 (mtpt)
REVERT: A  755 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8430 (t)
REVERT: A  827 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8054 (ptmm)
REVERT: A  976 LYS cc_start: 0.7379 (mttt) cc_final: 0.7159 (mmmm)
REVERT: A 1033 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7039 (tpp80)
REVERT: A 1153 GLN cc_start: 0.6752 (mm-40) cc_final: 0.6363 (mt0)
  outliers start: 31
  outliers final: 22
  residues processed: 158
  average time/residue: 0.0969
  time to fit residues: 24.0189
Evaluate side-chains
  155 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 126
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 CYS
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  506 GLU
Chi-restraints excluded: chain B residue  703 LEU
Chi-restraints excluded: chain B residue  755 SER
Chi-restraints excluded: chain B residue  825 THR
Chi-restraints excluded: chain B residue  898 THR
Chi-restraints excluded: chain B residue  913 VAL
Chi-restraints excluded: chain B residue 1033 ARG
Chi-restraints excluded: chain B residue 1044 GLU
Chi-restraints excluded: chain B residue 1056 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  506 GLU
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  755 SER
Chi-restraints excluded: chain A residue  768 ILE
Chi-restraints excluded: chain A residue  825 THR
Chi-restraints excluded: chain A residue  827 LYS
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue 1033 ARG
Chi-restraints excluded: chain A residue 1044 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1177 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 93 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 77 optimal weight:    4.9990
   chunk 97 optimal weight:    0.0470
   chunk 76 optimal weight:    3.9990
   chunk 139 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.9480

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

Flipped N/Q/H residues before XYZ refinement:
** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.136394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.113899 restraints weight = 21369.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.116928 restraints weight = 12533.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.119061 restraints weight = 8709.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.120518 restraints weight = 6751.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.121526 restraints weight = 5660.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.6308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13908  Z= 0.144
  Angle     :  0.544   9.892  19030  Z= 0.285
  Chirality :  0.039   0.146   2094
  Planarity :  0.004   0.033   2220
  Dihedral  : 18.029 136.471   2420
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.30 %
    Favored  : 79.52 %
  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 aren not related in a simple way.
  whole:  0.23 (0.23), residues: 1512
  helix:  1.99 (0.20), residues: 716
  sheet: -1.22 (0.42), residues: 180
  loop : -1.71 (0.25), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 478 
 TYR   0.026   0.001   TYR A1127 
 PHE   0.010   0.001   PHE B 790 
 TRP   0.009   0.001   TRP B 664 
 HIS   0.005   0.001   HIS B 605 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (13908)
  covalent geometry    : angle       0.54387 (19030)
  hydrogen bonds       : bond        0.03866 (  591)
  hydrogen bonds       : angle       3.79051 ( 1628)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 0.353 
Fit side-chains
REVERT: B  461 GLU cc_start: 0.7744 (pt0) cc_final: 0.7364 (pt0)
REVERT: B  669 MET cc_start: 0.8577 (mtp) cc_final: 0.8121 (mtp)
REVERT: B  976 LYS cc_start: 0.7394 (mttt) cc_final: 0.7171 (mmmm)
REVERT: B 1033 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7019 (tpp80)
REVERT: B 1153 GLN cc_start: 0.6743 (mm-40) cc_final: 0.6348 (mt0)
REVERT: A  461 GLU cc_start: 0.7794 (pt0) cc_final: 0.7420 (pt0)
REVERT: A  529 LYS cc_start: 0.7623 (tttt) cc_final: 0.7217 (mtpt)
REVERT: A  669 MET cc_start: 0.8591 (mtp) cc_final: 0.8192 (mtp)
REVERT: A  827 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7978 (ptmm)
REVERT: A 1033 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7054 (tpp80)
REVERT: A 1153 GLN cc_start: 0.6731 (mm-40) cc_final: 0.6349 (mt0)
  outliers start: 29
  outliers final: 22
  residues processed: 153
  average time/residue: 0.0939
  time to fit residues: 22.3126
Evaluate side-chains
  147 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 CYS
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  703 LEU
Chi-restraints excluded: chain B residue  768 ILE
Chi-restraints excluded: chain B residue  825 THR
Chi-restraints excluded: chain B residue  898 THR
Chi-restraints excluded: chain B residue  913 VAL
Chi-restraints excluded: chain B residue 1033 ARG
Chi-restraints excluded: chain B residue 1044 GLU
Chi-restraints excluded: chain B residue 1056 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  825 THR
Chi-restraints excluded: chain A residue  827 LYS
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue 1033 ARG
Chi-restraints excluded: chain A residue 1044 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1177 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7131 > 50:
  distance: 59 - 63:  22.457
  distance: 63 - 64:  14.918
  distance: 64 - 65:  29.046
  distance: 65 - 66:  15.164
  distance: 65 - 67:  25.443
  distance: 67 - 68:   6.015
  distance: 68 - 69:  15.929
  distance: 68 - 71:  11.586
  distance: 69 - 70:  11.415
  distance: 69 - 76:  11.592
  distance: 71 - 72:  24.107
  distance: 72 - 73:  16.244
  distance: 73 - 74:  39.045
  distance: 73 - 75:  25.338
  distance: 76 - 77:  43.383
  distance: 77 - 78:  15.531
  distance: 77 - 80:  45.780
  distance: 78 - 85:  16.816
  distance: 82 - 84:  40.381
  distance: 85 - 86:  43.456
  distance: 85 - 91:  17.258
  distance: 86 - 87:  40.678
  distance: 86 - 89:   5.021
  distance: 87 - 92:  14.502
  distance: 90 - 91:  30.670
  distance: 92 - 93:  28.502
  distance: 93 - 94:   8.135
  distance: 93 - 96:  15.122
  distance: 94 - 95:  26.921
  distance: 94 - 100:  22.624
  distance: 96 - 97:  45.259
  distance: 97 - 98:  23.782
  distance: 97 - 99:  22.026
  distance: 100 - 101:  33.528
  distance: 100 - 106:  18.344
  distance: 101 - 104:   7.429
  distance: 102 - 103:   9.245
  distance: 104 - 105:  30.971
  distance: 105 - 106:  31.260
  distance: 107 - 108:  43.558
  distance: 108 - 109:  22.217
  distance: 108 - 111:  18.729
  distance: 111 - 112:  39.799
  distance: 113 - 114:  39.655
  distance: 115 - 116:  42.628
  distance: 116 - 117:   5.902
  distance: 116 - 119:   6.960
  distance: 117 - 118:  40.172
  distance: 117 - 123:  15.568
  distance: 119 - 120:  42.895
  distance: 120 - 121:  32.693
  distance: 120 - 122:  22.934
  distance: 123 - 124:  25.666
  distance: 123 - 129:   4.134
  distance: 124 - 125:  25.362
  distance: 124 - 127:   7.163
  distance: 125 - 126:  10.728
  distance: 125 - 130:   8.694
  distance: 127 - 128:  32.264
  distance: 130 - 131:  16.994
  distance: 131 - 132:  28.666
  distance: 131 - 134:  16.112
  distance: 132 - 136:  35.504
  distance: 134 - 135:  29.774