Starting phenix.real_space_refine
on Wed May 14 18:31:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kgp_37229/05_2025/8kgp_37229.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kgp_37229/05_2025/8kgp_37229.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kgp_37229/05_2025/8kgp_37229.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kgp_37229/05_2025/8kgp_37229.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kgp_37229/05_2025/8kgp_37229.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kgp_37229/05_2025/8kgp_37229.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    7822      2.51       5
     N    2092      2.21       5
     O    2204      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12168
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 6084
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 749, 6084
          Classifications: {'peptide': 749}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 718}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 6084
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 749, 6084
          Classifications: {'peptide': 749}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 718}
          Chain breaks: 2
  Time building chain proxies: 7.82, per 1000 atoms: 0.64
  Number of scatterers: 12168
  At special positions: 0
  Unit cell: (113.75, 117.65, 113.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    2204      8.00
     N    2092      7.00
     C    7822      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: 2.82
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2812

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 14 sheets defined
      46.4% alpha, 9.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'B' and resid 441 through 451
      removed outlier: 3.780A  pdb=" N   THR B 451 " --> pdb=" O   ARG B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 513
      removed outlier: 3.768A  pdb=" N   GLN B 510 " --> pdb=" O   GLN B 506 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL B 511 " --> pdb=" O   GLY B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 560
      removed outlier: 4.506A  pdb=" N   LEU B 549 " --> pdb=" O   CYS B 545 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLY B 550 " --> pdb=" O   GLY B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 565
      removed outlier: 4.184A  pdb=" N   ILE B 564 " --> pdb=" O   TRP B 560 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ILE B 565 " --> pdb=" O   PRO B 561 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 560 through 565'
    Processing helix  chain 'B' and resid 593 through 601
      removed outlier: 3.749A  pdb=" N   TRP B 599 " --> pdb=" O   GLU B 595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 616 through 620
      removed outlier: 3.901A  pdb=" N   HIS B 620 " --> pdb=" O   LEU B 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 621 through 629
      removed outlier: 3.695A  pdb=" N   PHE B 629 " --> pdb=" O   VAL B 625 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 632 through 634
      No H-bonds generated for 'chain 'B' and resid 632 through 634'
    Processing helix  chain 'B' and resid 644 through 653
      removed outlier: 3.576A  pdb=" N   PHE B 653 " --> pdb=" O   PHE B 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 656 through 664
    Processing helix  chain 'B' and resid 672 through 683
      removed outlier: 3.970A  pdb=" N   VAL B 682 " --> pdb=" O   SER B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 695
    Processing helix  chain 'B' and resid 695 through 703
      removed outlier: 3.747A  pdb=" N   ILE B 703 " --> pdb=" O   LYS B 699 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 715 through 729
    Processing helix  chain 'B' and resid 738 through 749
    Processing helix  chain 'B' and resid 755 through 766
      removed outlier: 3.780A  pdb=" N   ALA B 766 " --> pdb=" O   ILE B 762 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 787 through 791
      removed outlier: 3.857A  pdb=" N   LEU B 790 " --> pdb=" O   SER B 787 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLY B 791 " --> pdb=" O   ARG B 788 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 787 through 791'
    Processing helix  chain 'B' and resid 809 through 814
      removed outlier: 3.812A  pdb=" N   PHE B 814 " --> pdb=" O   ILE B 810 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 815 through 819
      removed outlier: 3.601A  pdb=" N   SER B 819 " --> pdb=" O   ALA B 816 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 864 through 877
      removed outlier: 3.812A  pdb=" N   ALA B 870 " --> pdb=" O   GLU B 866 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   LEU B 871 " --> pdb=" O   ASP B 867 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ASP B 877 " --> pdb=" O   ARG B 873 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 882 through 888
      removed outlier: 3.652A  pdb=" N   LEU B 885 " --> pdb=" O   LYS B 882 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   LEU B 886 " --> pdb=" O   HIS B 883 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 942 through 953
      removed outlier: 3.821A  pdb=" N   SER B 953 " --> pdb=" O   SER B 949 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 953 through 958
    Processing helix  chain 'B' and resid 982 through 990
      removed outlier: 3.845A  pdb=" N   VAL B 987 " --> pdb=" O   LEU B 983 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   GLU B 988 " --> pdb=" O   ASN B 984 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 998 through 1003
      removed outlier: 3.513A  pdb=" N   PHE B1002 " --> pdb=" O   SER B 998 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1028 through 1070
      removed outlier: 3.662A  pdb=" N   LEU B1032 " --> pdb=" O   TYR B1028 " (cutoff:3.500A)
      Proline residue:  B1037  - end of helix
      removed outlier: 3.694A  pdb=" N   ARG B1040 " --> pdb=" O   LEU B1036 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU B1041 " --> pdb=" O   PRO B1037 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1081 through 1092
      removed outlier: 3.577A  pdb=" N   GLU B1091 " --> pdb=" O   ARG B1087 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   HIS B1092 " --> pdb=" O   ILE B1088 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1098 through 1104
    Processing helix  chain 'B' and resid 1109 through 1117
    Processing helix  chain 'B' and resid 1134 through 1159
      removed outlier: 3.742A  pdb=" N   LYS B1138 " --> pdb=" O   LEU B1134 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   THR B1139 " --> pdb=" O   ILE B1135 " (cutoff:3.500A)
      removed outlier: 5.269A  pdb=" N   ARG B1140 " --> pdb=" O   ALA B1136 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ARG B1141 " --> pdb=" O   ALA B1137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1166 through 1186
      removed outlier: 4.152A  pdb=" N   GLU B1172 " --> pdb=" O   SER B1168 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASN B1186 " --> pdb=" O   ILE B1182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 451
      removed outlier: 3.705A  pdb=" N   SER A 444 " --> pdb=" O   ASP A 440 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   THR A 451 " --> pdb=" O   ARG A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 513
      removed outlier: 3.772A  pdb=" N   GLN A 510 " --> pdb=" O   GLN A 506 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL A 511 " --> pdb=" O   GLY A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 560
      removed outlier: 4.508A  pdb=" N   LEU A 549 " --> pdb=" O   CYS A 545 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLY A 550 " --> pdb=" O   GLY A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 565
      removed outlier: 4.183A  pdb=" N   ILE A 564 " --> pdb=" O   TRP A 560 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ILE A 565 " --> pdb=" O   PRO A 561 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 560 through 565'
    Processing helix  chain 'A' and resid 593 through 601
      removed outlier: 3.751A  pdb=" N   TRP A 599 " --> pdb=" O   GLU A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 620
      removed outlier: 3.905A  pdb=" N   HIS A 620 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 629
      removed outlier: 3.711A  pdb=" N   PHE A 629 " --> pdb=" O   VAL A 625 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 634
      No H-bonds generated for 'chain 'A' and resid 632 through 634'
    Processing helix  chain 'A' and resid 644 through 653
      removed outlier: 3.575A  pdb=" N   PHE A 653 " --> pdb=" O   PHE A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 664
    Processing helix  chain 'A' and resid 672 through 683
      removed outlier: 3.970A  pdb=" N   VAL A 682 " --> pdb=" O   SER A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 695
    Processing helix  chain 'A' and resid 695 through 703
      removed outlier: 3.747A  pdb=" N   ILE A 703 " --> pdb=" O   LYS A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 729
    Processing helix  chain 'A' and resid 738 through 749
    Processing helix  chain 'A' and resid 755 through 765
    Processing helix  chain 'A' and resid 787 through 791
      removed outlier: 3.909A  pdb=" N   LEU A 790 " --> pdb=" O   SER A 787 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   GLY A 791 " --> pdb=" O   ARG A 788 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 787 through 791'
    Processing helix  chain 'A' and resid 809 through 814
      removed outlier: 3.812A  pdb=" N   PHE A 814 " --> pdb=" O   ILE A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 815 through 819
      removed outlier: 3.600A  pdb=" N   SER A 819 " --> pdb=" O   ALA A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 864 through 877
      removed outlier: 3.814A  pdb=" N   ALA A 870 " --> pdb=" O   GLU A 866 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   LEU A 871 " --> pdb=" O   ASP A 867 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ASP A 877 " --> pdb=" O   ARG A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 882 through 888
      removed outlier: 3.652A  pdb=" N   LEU A 885 " --> pdb=" O   LYS A 882 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LEU A 886 " --> pdb=" O   HIS A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 953
      removed outlier: 3.823A  pdb=" N   SER A 953 " --> pdb=" O   SER A 949 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 through 958
      removed outlier: 3.502A  pdb=" N   THR A 958 " --> pdb=" O   SER A 954 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 990
      removed outlier: 3.850A  pdb=" N   VAL A 987 " --> pdb=" O   LEU A 983 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   GLU A 988 " --> pdb=" O   ASN A 984 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1003
    Processing helix  chain 'A' and resid 1028 through 1070
      removed outlier: 3.660A  pdb=" N   LEU A1032 " --> pdb=" O   TYR A1028 " (cutoff:3.500A)
      Proline residue:  A1037  - end of helix
      removed outlier: 3.698A  pdb=" N   ARG A1040 " --> pdb=" O   LEU A1036 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLU A1041 " --> pdb=" O   PRO A1037 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1075 through 1079
      removed outlier: 3.837A  pdb=" N   HIS A1078 " --> pdb=" O   ASN A1075 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1081 through 1092
      removed outlier: 3.565A  pdb=" N   GLU A1091 " --> pdb=" O   ARG A1087 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   HIS A1092 " --> pdb=" O   ILE A1088 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1098 through 1104
    Processing helix  chain 'A' and resid 1109 through 1117
    Processing helix  chain 'A' and resid 1134 through 1159
      removed outlier: 3.745A  pdb=" N   LYS A1138 " --> pdb=" O   LEU A1134 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   THR A1139 " --> pdb=" O   ILE A1135 " (cutoff:3.500A)
      removed outlier: 5.328A  pdb=" N   ARG A1140 " --> pdb=" O   ALA A1136 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ARG A1141 " --> pdb=" O   ALA A1137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1166 through 1186
      removed outlier: 4.153A  pdb=" N   GLU A1172 " --> pdb=" O   SER A1168 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASN A1186 " --> pdb=" O   ILE A1182 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 465 through 469
      removed outlier: 5.764A  pdb=" N   VAL B 569 " --> pdb=" O   PHE B 639 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   ILE B 685 " --> pdb=" O   VAL B 636 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   THR B 638 " --> pdb=" O   ILE B 685 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 588 through 590
    Processing sheet with id=AA3, first strand: chain 'B' and resid 736 through 737
    Processing sheet with id=AA4, first strand: chain 'B' and resid 824 through 827
      removed outlier: 5.059A  pdb=" N   GLU B 833 " --> pdb=" O   VAL B 825 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   GLU B 827 " --> pdb=" O   ARG B 831 " (cutoff:3.500A)
      removed outlier: 5.570A  pdb=" N   ARG B 831 " --> pdb=" O   GLU B 827 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 909 through 913
      removed outlier: 3.680A  pdb=" N   HIS B 909 " --> pdb=" O   TYR B 920 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   TYR B 916 " --> pdb=" O   PHE B 913 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 922 through 925
      removed outlier: 6.155A  pdb=" N   THR B 922 " --> pdb=" O   THR B 935 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1013 through 1015
      removed outlier: 4.513A  pdb=" N   LEU B1013 " --> pdb=" O   PHE B1025 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 465 through 469
      removed outlier: 5.765A  pdb=" N   VAL A 569 " --> pdb=" O   PHE A 639 " (cutoff:3.500A)
      removed outlier: 8.269A  pdb=" N   ILE A 685 " --> pdb=" O   VAL A 636 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   THR A 638 " --> pdb=" O   ILE A 685 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 590
    Processing sheet with id=AB1, first strand: chain 'A' and resid 736 through 737
    Processing sheet with id=AB2, first strand: chain 'A' and resid 824 through 827
      removed outlier: 5.048A  pdb=" N   GLU A 833 " --> pdb=" O   VAL A 825 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   GLU A 827 " --> pdb=" O   ARG A 831 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   ARG A 831 " --> pdb=" O   GLU A 827 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 909 through 913
      removed outlier: 3.680A  pdb=" N   HIS A 909 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   TYR A 916 " --> pdb=" O   PHE A 913 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 922 through 925
      removed outlier: 6.156A  pdb=" N   THR A 922 " --> pdb=" O   THR A 935 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1013 through 1015
      removed outlier: 4.513A  pdb=" N   LEU A1013 " --> pdb=" O   PHE A1025 " (cutoff:3.500A)

    465 hydrogen bonds defined for protein.
    1338 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.49

  Time building geometry restraints manager: 3.33 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3304
        1.33 -     1.45: 2369
        1.45 -     1.57: 6707
        1.57 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 12458
  Sorted by residual:
  bond pdb=" N   LEU B1036 "
       pdb=" CA  LEU B1036 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.04e-02 9.25e+03 9.23e+00
  bond pdb=" N   ILE B 763 "
       pdb=" CA  ILE B 763 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.036 1.21e-02 6.83e+03 8.79e+00
  bond pdb=" N   LEU A1036 "
       pdb=" CA  LEU A1036 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.04e-02 9.25e+03 8.68e+00
  bond pdb=" N   ILE A1031 "
       pdb=" CA  ILE A1031 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.033 1.19e-02 7.06e+03 7.50e+00
  bond pdb=" N   TYR A 848 "
       pdb=" CA  TYR A 848 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.033 1.23e-02 6.61e+03 7.23e+00
  ... (remaining 12453 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 16081
        2.32 -     4.64: 660
        4.64 -     6.96: 64
        6.96 -     9.28: 18
        9.28 -    11.60: 3
  Bond angle restraints: 16826
  Sorted by residual:
  angle pdb=" C   ARG A 929 "
        pdb=" N   ASN A 930 "
        pdb=" CA  ASN A 930 "
      ideal   model   delta    sigma   weight residual
     122.82  129.74   -6.92 1.42e+00 4.96e-01 2.37e+01
  angle pdb=" C   ARG B 929 "
        pdb=" N   ASN B 930 "
        pdb=" CA  ASN B 930 "
      ideal   model   delta    sigma   weight residual
     122.82  129.73   -6.91 1.42e+00 4.96e-01 2.37e+01
  angle pdb=" C   SER A 902 "
        pdb=" N   ASN A 903 "
        pdb=" CA  ASN A 903 "
      ideal   model   delta    sigma   weight residual
     121.54  129.65   -8.11 1.91e+00 2.74e-01 1.80e+01
  angle pdb=" C   SER B 902 "
        pdb=" N   ASN B 903 "
        pdb=" CA  ASN B 903 "
      ideal   model   delta    sigma   weight residual
     121.54  129.65   -8.11 1.91e+00 2.74e-01 1.80e+01
  angle pdb=" C   ILE A 565 "
        pdb=" N   HIS A 566 "
        pdb=" CA  HIS A 566 "
      ideal   model   delta    sigma   weight residual
     121.54  129.36   -7.82 1.91e+00 2.74e-01 1.68e+01
  ... (remaining 16821 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.26: 6868
       14.26 -    28.51: 447
       28.51 -    42.77: 129
       42.77 -    57.02: 20
       57.02 -    71.28: 10
  Dihedral angle restraints: 7474
    sinusoidal: 3086
      harmonic: 4388
  Sorted by residual:
  dihedral pdb=" CA  PRO A 901 "
           pdb=" C   PRO A 901 "
           pdb=" N   SER A 902 "
           pdb=" CA  SER A 902 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.80  -25.20     0      5.00e+00 4.00e-02 2.54e+01
  dihedral pdb=" CA  PRO B 901 "
           pdb=" C   PRO B 901 "
           pdb=" N   SER B 902 "
           pdb=" CA  SER B 902 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.82  -25.18     0      5.00e+00 4.00e-02 2.54e+01
  dihedral pdb=" CA  THR A 695 "
           pdb=" C   THR A 695 "
           pdb=" N   LYS A 696 "
           pdb=" CA  LYS A 696 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.45   20.55     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 7471 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1420
       0.074 -    0.149: 359
       0.149 -    0.223: 23
       0.223 -    0.298: 14
       0.298 -    0.372: 2
  Chirality restraints: 1818
  Sorted by residual:
  chirality pdb=" CB  ILE A 963 "
            pdb=" CA  ILE A 963 "
            pdb=" CG1 ILE A 963 "
            pdb=" CG2 ILE A 963 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.37 2.00e-01 2.50e+01 3.46e+00
  chirality pdb=" CB  ILE B 685 "
            pdb=" CA  ILE B 685 "
            pdb=" CG1 ILE B 685 "
            pdb=" CG2 ILE B 685 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" CB  ILE A 685 "
            pdb=" CA  ILE A 685 "
            pdb=" CG1 ILE A 685 "
            pdb=" CG2 ILE A 685 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.19e+00
  ... (remaining 1815 not shown)

  Planarity restraints: 2144
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B1170 "   -0.023 2.00e-02 2.50e+03   2.50e-02 1.56e+01
        pdb=" CG  TRP B1170 "    0.065 2.00e-02 2.50e+03
        pdb=" CD1 TRP B1170 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD2 TRP B1170 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B1170 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B1170 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B1170 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B1170 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B1170 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B1170 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1170 "    0.023 2.00e-02 2.50e+03   2.50e-02 1.56e+01
        pdb=" CG  TRP A1170 "   -0.065 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1170 "    0.036 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1170 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1170 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1170 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1170 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1170 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1170 "    0.011 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1170 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 824 "   -0.027 2.00e-02 2.50e+03   2.38e-02 1.13e+01
        pdb=" CG  TYR A 824 "    0.057 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 824 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 824 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 824 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 824 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 824 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 824 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 2141 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 3771
        2.83 -     3.35: 10055
        3.35 -     3.87: 18690
        3.87 -     4.38: 21819
        4.38 -     4.90: 38780
  Nonbonded interactions: 93115
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 946 "
            pdb=" O   LEU A1003 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OH  TYR B 946 "
            pdb=" O   LEU B1003 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   VAL B 840 "
            pdb=" CH2 TRP B1035 "
     model   vdw
     2.330 3.340
  nonbonded pdb=" OG1 THR A 922 "
            pdb=" OG1 THR A 935 "
     model   vdw
     2.340 3.040
  nonbonded pdb=" OG1 THR B 922 "
            pdb=" OG1 THR B 935 "
     model   vdw
     2.341 3.040
  ... (remaining 93110 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.320
  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:          0.560
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     29.050
  Find NCS groups from input model:        0.530
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
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   0.075  12458  Z= 0.457
  Angle     :  1.053  11.602  16826  Z= 0.590
  Chirality :  0.066   0.372   1818
  Planarity :  0.007   0.065   2144
  Dihedral  : 11.202  71.281   4662
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  4.96 %
    Favored  : 94.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.96 (0.18), residues: 1486
  helix: -2.64 (0.16), residues: 598
  sheet: -1.81 (0.35), residues: 218
  loop : -2.81 (0.20), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.004   TRP A1170 
 HIS   0.015   0.002   HIS B1192 
 PHE   0.046   0.004   PHE B 785 
 TYR   0.057   0.004   TYR A 824 
 ARG   0.015   0.002   ARG A 578 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18670 (  465)
  hydrogen bonds       : angle       6.85743 ( 1338)
  covalent geometry    : bond        0.01083 (12458)
  covalent geometry    : angle       1.05316 (16826)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 276
  time to evaluate  : 1.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  747 ASP cc_start: 0.8578 (t70) cc_final: 0.8336 (t0)
REVERT: B  977 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7577 (tttm)
REVERT: A  573 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7715 (mp)
REVERT: A  747 ASP cc_start: 0.8591 (t70) cc_final: 0.8370 (t0)
REVERT: A  964 ILE cc_start: 0.8994 (mt) cc_final: 0.8729 (mm)
REVERT: A  977 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7330 (tttm)
  outliers start: 10
  outliers final: 1
  residues processed: 282
  average time/residue: 0.2930
  time to fit residues: 111.5892
Evaluate side-chains
  147 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 145
  time to evaluate  : 1.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  574 THR
Chi-restraints excluded: chain A residue  573 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 75 optimal weight:   10.0000
   chunk 59 optimal weight:    0.7980
   chunk 116 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0570
   chunk 70 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 134 optimal weight:    0.9980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
B 620 HIS
B 634 ASN
B1119 GLN
B1157 GLN
A 620 HIS
A 634 ASN
A1051 HIS
A1119 GLN
A1157 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.135725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.101369 restraints weight = 16122.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 2.10
r_work: 0.2866 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2731 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12458  Z= 0.116
  Angle     :  0.574   9.231  16826  Z= 0.297
  Chirality :  0.042   0.180   1818
  Planarity :  0.005   0.041   2144
  Dihedral  :  4.926  37.128   1665
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 10.53 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.20), residues: 1486
  helix: -0.88 (0.19), residues: 612
  sheet: -1.29 (0.36), residues: 202
  loop : -2.27 (0.21), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A1170 
 HIS   0.005   0.001   HIS A 650 
 PHE   0.013   0.001   PHE B 559 
 TYR   0.014   0.001   TYR B 888 
 ARG   0.005   0.001   ARG B 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04577 (  465)
  hydrogen bonds       : angle       4.58717 ( 1338)
  covalent geometry    : bond        0.00263 (12458)
  covalent geometry    : angle       0.57419 (16826)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 1.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  551 LEU cc_start: 0.8994 (mp) cc_final: 0.8636 (tt)
REVERT: B  747 ASP cc_start: 0.9016 (t70) cc_final: 0.8727 (t0)
REVERT: B  977 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7443 (tttm)
REVERT: B 1064 ILE cc_start: 0.8107 (mt) cc_final: 0.7857 (mt)
REVERT: B 1134 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.6045 (pp)
REVERT: A  417 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8622 (mtpp)
REVERT: A  551 LEU cc_start: 0.8973 (mp) cc_final: 0.8605 (tt)
REVERT: A  612 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8468 (mtpp)
REVERT: A  673 GLU cc_start: 0.7902 (tp30) cc_final: 0.7672 (tp30)
REVERT: A  747 ASP cc_start: 0.9010 (t70) cc_final: 0.8774 (t0)
REVERT: A  957 MET cc_start: 0.9056 (mmm) cc_final: 0.8719 (tpt)
REVERT: A  964 ILE cc_start: 0.8995 (mt) cc_final: 0.8664 (mm)
REVERT: A  977 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7344 (tttp)
REVERT: A 1064 ILE cc_start: 0.8094 (mt) cc_final: 0.7850 (mt)
REVERT: A 1134 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.6059 (pp)
  outliers start: 19
  outliers final: 8
  residues processed: 201
  average time/residue: 0.2434
  time to fit residues: 69.7567
Evaluate side-chains
  157 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 147
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  540 GLN
Chi-restraints excluded: chain B residue  644 SER
Chi-restraints excluded: chain B residue  833 GLU
Chi-restraints excluded: chain B residue 1111 GLU
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  644 SER
Chi-restraints excluded: chain A residue  998 SER
Chi-restraints excluded: chain A residue 1111 GLU
Chi-restraints excluded: chain A residue 1134 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 147 optimal weight:    1.9990
   chunk 67 optimal weight:    9.9990
   chunk 92 optimal weight:    6.9990
   chunk 122 optimal weight:    3.9990
   chunk 108 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 123 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B1119 GLN
A1119 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.128404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.094100 restraints weight = 16621.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 2.16
r_work: 0.2726 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2588 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8812
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.084  12458  Z= 0.290
  Angle     :  0.696  14.172  16826  Z= 0.350
  Chirality :  0.049   0.161   1818
  Planarity :  0.005   0.050   2144
  Dihedral  :  4.935  19.235   1662
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 12.52 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.21), residues: 1486
  helix: -0.19 (0.21), residues: 620
  sheet: -1.24 (0.35), residues: 202
  loop : -2.12 (0.22), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B1170 
 HIS   0.009   0.002   HIS A1192 
 PHE   0.020   0.002   PHE B 785 
 TYR   0.029   0.002   TYR A 824 
 ARG   0.003   0.001   ARG B 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05645 (  465)
  hydrogen bonds       : angle       4.55231 ( 1338)
  covalent geometry    : bond        0.00729 (12458)
  covalent geometry    : angle       0.69560 (16826)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 151
  time to evaluate  : 1.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  417 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8593 (mtpp)
REVERT: B  515 ASP cc_start: 0.8320 (t70) cc_final: 0.7552 (p0)
REVERT: B  582 LYS cc_start: 0.8177 (mttm) cc_final: 0.7860 (mtmm)
REVERT: B  747 ASP cc_start: 0.9094 (t70) cc_final: 0.8866 (t0)
REVERT: B  817 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8668 (pm20)
REVERT: B  833 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7880 (pp20)
REVERT: B  977 LYS cc_start: 0.8249 (ttmt) cc_final: 0.7616 (tttm)
REVERT: B 1055 LYS cc_start: 0.8483 (mmmt) cc_final: 0.8209 (mtmt)
REVERT: B 1134 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.6058 (pp)
REVERT: A  417 LYS cc_start: 0.8953 (mtmt) cc_final: 0.8602 (mtpp)
REVERT: A  515 ASP cc_start: 0.8314 (t70) cc_final: 0.7548 (p0)
REVERT: A  582 LYS cc_start: 0.8214 (mttm) cc_final: 0.7908 (mtmm)
REVERT: A  977 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7471 (tttp)
REVERT: A 1134 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6046 (pp)
  outliers start: 38
  outliers final: 22
  residues processed: 180
  average time/residue: 0.2188
  time to fit residues: 58.1096
Evaluate side-chains
  162 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 1.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  608 ASN
Chi-restraints excluded: chain B residue  644 SER
Chi-restraints excluded: chain B residue  731 SER
Chi-restraints excluded: chain B residue  790 LEU
Chi-restraints excluded: chain B residue  817 GLU
Chi-restraints excluded: chain B residue  833 GLU
Chi-restraints excluded: chain B residue  890 ILE
Chi-restraints excluded: chain B residue  949 SER
Chi-restraints excluded: chain B residue 1065 VAL
Chi-restraints excluded: chain B residue 1111 GLU
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain B residue 1142 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  624 GLU
Chi-restraints excluded: chain A residue  644 SER
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  961 GLU
Chi-restraints excluded: chain A residue 1046 ARG
Chi-restraints excluded: chain A residue 1065 VAL
Chi-restraints excluded: chain A residue 1111 GLU
Chi-restraints excluded: chain A residue 1134 LEU
Chi-restraints excluded: chain A residue 1142 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 73 optimal weight:    0.7980
   chunk 69 optimal weight:    6.9990
   chunk 13 optimal weight:    0.0670
   chunk 127 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 115 optimal weight:    6.9990
   chunk 80 optimal weight:    4.9990
   chunk 118 optimal weight:    6.9990
   chunk 88 optimal weight:    0.9980
   overall best weight:    0.5718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.134677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.100250 restraints weight = 16233.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.08
r_work: 0.2839 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.2801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12458  Z= 0.095
  Angle     :  0.504   9.732  16826  Z= 0.254
  Chirality :  0.041   0.131   1818
  Planarity :  0.003   0.033   2144
  Dihedral  :  4.174  14.185   1662
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.59 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.22), residues: 1486
  helix:  0.54 (0.22), residues: 612
  sheet: -0.73 (0.36), residues: 196
  loop : -1.85 (0.22), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B1170 
 HIS   0.006   0.001   HIS A 650 
 PHE   0.011   0.001   PHE A 710 
 TYR   0.010   0.001   TYR A1124 
 ARG   0.003   0.000   ARG B 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03507 (  465)
  hydrogen bonds       : angle       4.25147 ( 1338)
  covalent geometry    : bond        0.00214 (12458)
  covalent geometry    : angle       0.50421 (16826)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 173
  time to evaluate  : 1.268 
Fit side-chains
   revert: symmetry clash
REVERT: B  747 ASP cc_start: 0.9027 (t70) cc_final: 0.8757 (t0)
REVERT: B  817 GLU cc_start: 0.9042 (pt0) cc_final: 0.8630 (pm20)
REVERT: B  977 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7565 (tttm)
REVERT: B 1134 LEU cc_start: 0.6387 (OUTLIER) cc_final: 0.6030 (pp)
REVERT: A  417 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8664 (mtpp)
REVERT: A  582 LYS cc_start: 0.8160 (mttm) cc_final: 0.7875 (mtmm)
REVERT: A  747 ASP cc_start: 0.9035 (t70) cc_final: 0.8773 (t0)
REVERT: A  890 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7570 (tt)
REVERT: A  977 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7484 (tttp)
REVERT: A 1134 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.5995 (pp)
  outliers start: 29
  outliers final: 15
  residues processed: 195
  average time/residue: 0.2334
  time to fit residues: 66.7471
Evaluate side-chains
  167 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  540 GLN
Chi-restraints excluded: chain B residue  551 LEU
Chi-restraints excluded: chain B residue  608 ASN
Chi-restraints excluded: chain B residue  644 SER
Chi-restraints excluded: chain B residue  731 SER
Chi-restraints excluded: chain B residue  890 ILE
Chi-restraints excluded: chain B residue 1111 GLU
Chi-restraints excluded: chain B residue 1123 THR
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  644 SER
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  961 GLU
Chi-restraints excluded: chain A residue 1111 GLU
Chi-restraints excluded: chain A residue 1123 THR
Chi-restraints excluded: chain A residue 1134 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 130 optimal weight:    7.9990
   chunk 93 optimal weight:    0.9990
   chunk 47 optimal weight:    8.9990
   chunk 44 optimal weight:    7.9990
   chunk 110 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 143 optimal weight:    0.1980
   chunk 84 optimal weight:    1.9990
   chunk 137 optimal weight:    0.0980
   chunk 118 optimal weight:    8.9990
   overall best weight:    0.8586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.134281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.099459 restraints weight = 16123.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 2.08
r_work: 0.2852 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2716 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12458  Z= 0.103
  Angle     :  0.500   9.469  16826  Z= 0.252
  Chirality :  0.041   0.135   1818
  Planarity :  0.003   0.032   2144
  Dihedral  :  3.958  13.895   1662
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 14.96 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.22), residues: 1486
  helix:  0.83 (0.22), residues: 618
  sheet: -0.45 (0.36), residues: 196
  loop : -1.68 (0.22), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B1170 
 HIS   0.007   0.001   HIS B1051 
 PHE   0.010   0.001   PHE A 710 
 TYR   0.011   0.001   TYR A 888 
 ARG   0.002   0.000   ARG B 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03485 (  465)
  hydrogen bonds       : angle       4.07356 ( 1338)
  covalent geometry    : bond        0.00242 (12458)
  covalent geometry    : angle       0.49985 (16826)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 1.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  417 LYS cc_start: 0.8923 (mtmt) cc_final: 0.8590 (mtpp)
REVERT: B  747 ASP cc_start: 0.9026 (t70) cc_final: 0.8754 (t0)
REVERT: B  817 GLU cc_start: 0.9051 (pt0) cc_final: 0.8612 (pm20)
REVERT: B  833 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7610 (pp20)
REVERT: B  977 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7534 (tttm)
REVERT: B 1134 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.6015 (pp)
REVERT: A  417 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8588 (mtpp)
REVERT: A  677 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7466 (mt0)
REVERT: A  747 ASP cc_start: 0.9016 (t70) cc_final: 0.8756 (t0)
REVERT: A  756 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7695 (tpt)
REVERT: A  977 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7444 (tttp)
REVERT: A 1134 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6056 (pp)
  outliers start: 27
  outliers final: 19
  residues processed: 173
  average time/residue: 0.2187
  time to fit residues: 56.3807
Evaluate side-chains
  167 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 1.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  540 GLN
Chi-restraints excluded: chain B residue  608 ASN
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  687 CYS
Chi-restraints excluded: chain B residue  731 SER
Chi-restraints excluded: chain B residue  833 GLU
Chi-restraints excluded: chain B residue  890 ILE
Chi-restraints excluded: chain B residue 1111 GLU
Chi-restraints excluded: chain B residue 1123 THR
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  644 SER
Chi-restraints excluded: chain A residue  677 GLN
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  961 GLU
Chi-restraints excluded: chain A residue 1111 GLU
Chi-restraints excluded: chain A residue 1123 THR
Chi-restraints excluded: chain A residue 1134 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 37 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 74 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   chunk 79 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 76 optimal weight:    4.9990
   chunk 147 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.131636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.096006 restraints weight = 16512.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 2.18
r_work: 0.2853 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8678
moved from start:          0.3162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12458  Z= 0.097
  Angle     :  0.487   9.406  16826  Z= 0.245
  Chirality :  0.041   0.132   1818
  Planarity :  0.003   0.028   2144
  Dihedral  :  3.784  12.915   1662
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 15.19 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.22), residues: 1486
  helix:  1.09 (0.22), residues: 618
  sheet: -0.22 (0.37), residues: 196
  loop : -1.61 (0.22), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 820 
 HIS   0.005   0.001   HIS B 650 
 PHE   0.010   0.001   PHE A 710 
 TYR   0.010   0.001   TYR A 888 
 ARG   0.003   0.000   ARG B 578 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03271 (  465)
  hydrogen bonds       : angle       3.97809 ( 1338)
  covalent geometry    : bond        0.00227 (12458)
  covalent geometry    : angle       0.48680 (16826)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 156
  time to evaluate  : 1.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  756 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7858 (tpt)
REVERT: B  817 GLU cc_start: 0.9052 (pt0) cc_final: 0.8575 (pm20)
REVERT: B  833 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7571 (pp20)
REVERT: B  977 LYS cc_start: 0.8047 (ttmt) cc_final: 0.7421 (tttm)
REVERT: B 1134 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.5867 (mt)
REVERT: A  677 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7405 (mt0)
REVERT: A  756 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7624 (tpt)
REVERT: A  977 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7313 (tttp)
REVERT: A 1134 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6054 (pp)
  outliers start: 28
  outliers final: 19
  residues processed: 175
  average time/residue: 0.2172
  time to fit residues: 56.4993
Evaluate side-chains
  171 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 146
  time to evaluate  : 1.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  540 GLN
Chi-restraints excluded: chain B residue  608 ASN
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  687 CYS
Chi-restraints excluded: chain B residue  731 SER
Chi-restraints excluded: chain B residue  756 MET
Chi-restraints excluded: chain B residue  833 GLU
Chi-restraints excluded: chain B residue  890 ILE
Chi-restraints excluded: chain B residue 1111 GLU
Chi-restraints excluded: chain B residue 1123 THR
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  644 SER
Chi-restraints excluded: chain A residue  677 GLN
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  961 GLU
Chi-restraints excluded: chain A residue 1111 GLU
Chi-restraints excluded: chain A residue 1123 THR
Chi-restraints excluded: chain A residue 1134 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 144 optimal weight:    2.9990
   chunk 115 optimal weight:    2.9990
   chunk 126 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
B 634 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.130011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.094251 restraints weight = 16464.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 2.14
r_work: 0.2800 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  12458  Z= 0.167
  Angle     :  0.543  12.417  16826  Z= 0.272
  Chirality :  0.043   0.142   1818
  Planarity :  0.004   0.034   2144
  Dihedral  :  4.003  15.561   1662
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 15.19 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.22), residues: 1486
  helix:  1.15 (0.22), residues: 622
  sheet: -0.30 (0.37), residues: 196
  loop : -1.65 (0.22), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 820 
 HIS   0.007   0.001   HIS B 650 
 PHE   0.010   0.001   PHE A 739 
 TYR   0.013   0.001   TYR B 824 
 ARG   0.005   0.000   ARG B 578 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04074 (  465)
  hydrogen bonds       : angle       4.08034 ( 1338)
  covalent geometry    : bond        0.00421 (12458)
  covalent geometry    : angle       0.54327 (16826)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 147
  time to evaluate  : 1.289 
Fit side-chains
REVERT: B  582 LYS cc_start: 0.8161 (mttm) cc_final: 0.7807 (mtmt)
REVERT: B  756 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7974 (tpt)
REVERT: B  817 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8607 (pm20)
REVERT: B  833 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7810 (pp20)
REVERT: B  977 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7481 (tttm)
REVERT: B 1134 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.5870 (mt)
REVERT: A  582 LYS cc_start: 0.8144 (mttm) cc_final: 0.7861 (mtmm)
REVERT: A  747 ASP cc_start: 0.9050 (t70) cc_final: 0.8811 (t0)
REVERT: A  756 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7715 (tpt)
REVERT: A  977 LYS cc_start: 0.8064 (ttmt) cc_final: 0.7377 (tttp)
REVERT: A 1134 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.5952 (mt)
  outliers start: 34
  outliers final: 24
  residues processed: 173
  average time/residue: 0.2205
  time to fit residues: 56.6287
Evaluate side-chains
  175 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 145
  time to evaluate  : 1.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  540 GLN
Chi-restraints excluded: chain B residue  608 ASN
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  644 SER
Chi-restraints excluded: chain B residue  687 CYS
Chi-restraints excluded: chain B residue  731 SER
Chi-restraints excluded: chain B residue  756 MET
Chi-restraints excluded: chain B residue  790 LEU
Chi-restraints excluded: chain B residue  817 GLU
Chi-restraints excluded: chain B residue  833 GLU
Chi-restraints excluded: chain B residue  890 ILE
Chi-restraints excluded: chain B residue 1123 THR
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  644 SER
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  961 GLU
Chi-restraints excluded: chain A residue 1111 GLU
Chi-restraints excluded: chain A residue 1123 THR
Chi-restraints excluded: chain A residue 1134 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 109 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0470
   chunk 16 optimal weight:    6.9990
   chunk 37 optimal weight:    0.7980
   chunk 136 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9980
   chunk 85 optimal weight:    0.6980
   chunk 8 optimal weight:    0.2980
   chunk 119 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   overall best weight:    0.5678

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.134666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.099717 restraints weight = 16287.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 2.09
r_work: 0.2811 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2679 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.3358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12458  Z= 0.087
  Angle     :  0.476   9.276  16826  Z= 0.240
  Chirality :  0.040   0.132   1818
  Planarity :  0.003   0.028   2144
  Dihedral  :  3.689  12.605   1662
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.34 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.22), residues: 1486
  helix:  1.42 (0.22), residues: 616
  sheet: -0.18 (0.37), residues: 196
  loop : -1.52 (0.22), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 820 
 HIS   0.006   0.001   HIS B 650 
 PHE   0.009   0.001   PHE A 710 
 TYR   0.011   0.001   TYR B 966 
 ARG   0.003   0.000   ARG A 912 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03088 (  465)
  hydrogen bonds       : angle       3.93949 ( 1338)
  covalent geometry    : bond        0.00198 (12458)
  covalent geometry    : angle       0.47556 (16826)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 154
  time to evaluate  : 1.252 
Fit side-chains
REVERT: B  551 LEU cc_start: 0.8993 (mp) cc_final: 0.8681 (tt)
REVERT: B  582 LYS cc_start: 0.8065 (mttm) cc_final: 0.7802 (mtmt)
REVERT: B  756 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7890 (tpt)
REVERT: B  817 GLU cc_start: 0.9062 (pt0) cc_final: 0.8612 (pm20)
REVERT: B  833 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7524 (pp20)
REVERT: B  977 LYS cc_start: 0.8022 (ttmt) cc_final: 0.7370 (tttm)
REVERT: B 1134 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.5933 (mt)
REVERT: A  582 LYS cc_start: 0.8093 (mttm) cc_final: 0.7793 (mtmm)
REVERT: A  977 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7358 (tttm)
REVERT: A 1134 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.5958 (mt)
  outliers start: 25
  outliers final: 19
  residues processed: 170
  average time/residue: 0.2231
  time to fit residues: 56.2929
Evaluate side-chains
  165 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 1.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  540 GLN
Chi-restraints excluded: chain B residue  608 ASN
Chi-restraints excluded: chain B residue  660 ARG
Chi-restraints excluded: chain B residue  687 CYS
Chi-restraints excluded: chain B residue  731 SER
Chi-restraints excluded: chain B residue  756 MET
Chi-restraints excluded: chain B residue  833 GLU
Chi-restraints excluded: chain B residue  890 ILE
Chi-restraints excluded: chain B residue  975 LEU
Chi-restraints excluded: chain B residue 1123 THR
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  660 ARG
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  961 GLU
Chi-restraints excluded: chain A residue 1111 GLU
Chi-restraints excluded: chain A residue 1123 THR
Chi-restraints excluded: chain A residue 1134 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 114 optimal weight:    0.9980
   chunk 137 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 146 optimal weight:    0.1980
   chunk 132 optimal weight:    0.6980
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B 634 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.133923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.099039 restraints weight = 16216.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 2.07
r_work: 0.2875 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.3376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12458  Z= 0.104
  Angle     :  0.481   9.564  16826  Z= 0.242
  Chirality :  0.041   0.134   1818
  Planarity :  0.003   0.028   2144
  Dihedral  :  3.680  12.792   1662
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.64 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.22), residues: 1486
  helix:  1.36 (0.22), residues: 632
  sheet: -0.18 (0.38), residues: 196
  loop : -1.48 (0.22), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.006   0.001   HIS B 650 
 PHE   0.009   0.001   PHE A 710 
 TYR   0.010   0.001   TYR A 888 
 ARG   0.003   0.000   ARG B 578 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03295 (  465)
  hydrogen bonds       : angle       3.91903 ( 1338)
  covalent geometry    : bond        0.00255 (12458)
  covalent geometry    : angle       0.48111 (16826)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 1.325 
Fit side-chains
REVERT: B  582 LYS cc_start: 0.8092 (mttm) cc_final: 0.7821 (mtmt)
REVERT: B  756 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7946 (tpt)
REVERT: B  817 GLU cc_start: 0.9052 (pt0) cc_final: 0.8608 (pm20)
REVERT: B  833 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7650 (pp20)
REVERT: B  977 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7438 (tttm)
REVERT: B 1134 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.5932 (mt)
REVERT: A  582 LYS cc_start: 0.8137 (mttm) cc_final: 0.7852 (mtmt)
REVERT: A  747 ASP cc_start: 0.9026 (t70) cc_final: 0.8775 (t0)
REVERT: A  977 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7339 (tttm)
REVERT: A 1134 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.5901 (mt)
  outliers start: 24
  outliers final: 19
  residues processed: 159
  average time/residue: 0.2289
  time to fit residues: 53.9769
Evaluate side-chains
  165 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 1.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  540 GLN
Chi-restraints excluded: chain B residue  608 ASN
Chi-restraints excluded: chain B residue  660 ARG
Chi-restraints excluded: chain B residue  687 CYS
Chi-restraints excluded: chain B residue  756 MET
Chi-restraints excluded: chain B residue  790 LEU
Chi-restraints excluded: chain B residue  833 GLU
Chi-restraints excluded: chain B residue  890 ILE
Chi-restraints excluded: chain B residue  963 ILE
Chi-restraints excluded: chain B residue 1123 THR
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  660 ARG
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  961 GLU
Chi-restraints excluded: chain A residue 1111 GLU
Chi-restraints excluded: chain A residue 1123 THR
Chi-restraints excluded: chain A residue 1134 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 139 optimal weight:    0.0570
   chunk 2 optimal weight:    0.5980
   chunk 39 optimal weight:    0.2980
   chunk 65 optimal weight:    0.0020
   chunk 93 optimal weight:    5.9990
   chunk 124 optimal weight:    0.0670
   chunk 99 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9980
   chunk 113 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   overall best weight:    0.2044

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

Flipped N/Q/H residues before XYZ refinement:
B 634 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.137376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.102851 restraints weight = 16077.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 2.07
r_work: 0.2933 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2801 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.3619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12458  Z= 0.079
  Angle     :  0.452   9.059  16826  Z= 0.231
  Chirality :  0.040   0.128   1818
  Planarity :  0.003   0.026   2144
  Dihedral  :  3.441  12.686   1662
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 17.10 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.23), residues: 1486
  helix:  1.59 (0.23), residues: 626
  sheet: -0.16 (0.38), residues: 198
  loop : -1.41 (0.23), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 820 
 HIS   0.007   0.001   HIS A 650 
 PHE   0.009   0.001   PHE A 710 
 TYR   0.014   0.001   TYR B 966 
 ARG   0.002   0.000   ARG B 912 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02640 (  465)
  hydrogen bonds       : angle       3.84908 ( 1338)
  covalent geometry    : bond        0.00169 (12458)
  covalent geometry    : angle       0.45219 (16826)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 1.525 
Fit side-chains
REVERT: B  551 LEU cc_start: 0.8989 (mp) cc_final: 0.8687 (tt)
REVERT: B  582 LYS cc_start: 0.8053 (mttm) cc_final: 0.7848 (mttt)
REVERT: B  661 LYS cc_start: 0.8592 (mttt) cc_final: 0.8020 (ptmm)
REVERT: B  756 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7886 (tpt)
REVERT: B  817 GLU cc_start: 0.9017 (pt0) cc_final: 0.8574 (pm20)
REVERT: B  977 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7381 (tttm)
REVERT: B 1134 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.5948 (mt)
REVERT: A  572 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8839 (mp)
REVERT: A  582 LYS cc_start: 0.8109 (mttm) cc_final: 0.7882 (mttt)
REVERT: A  661 LYS cc_start: 0.8570 (mttt) cc_final: 0.8002 (ptmm)
REVERT: A  890 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7288 (tt)
REVERT: A  977 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7220 (tttm)
REVERT: A 1111 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7999 (pm20)
REVERT: A 1134 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.5902 (mt)
  outliers start: 20
  outliers final: 14
  residues processed: 165
  average time/residue: 0.2492
  time to fit residues: 59.9169
Evaluate side-chains
  162 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 1.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  540 GLN
Chi-restraints excluded: chain B residue  608 ASN
Chi-restraints excluded: chain B residue  660 ARG
Chi-restraints excluded: chain B residue  687 CYS
Chi-restraints excluded: chain B residue  756 MET
Chi-restraints excluded: chain B residue  833 GLU
Chi-restraints excluded: chain B residue  890 ILE
Chi-restraints excluded: chain B residue  963 ILE
Chi-restraints excluded: chain B residue 1134 LEU
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  660 ARG
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  961 GLU
Chi-restraints excluded: chain A residue 1111 GLU
Chi-restraints excluded: chain A residue 1134 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 108 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 121 optimal weight:    7.9990
   chunk 101 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 131 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0870
   chunk 140 optimal weight:    0.9980
   overall best weight:    0.9360

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

Flipped N/Q/H residues before XYZ refinement:
B 634 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.135442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.100338 restraints weight = 16272.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.10
r_work: 0.2850 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  12458  Z= 0.102
  Angle     :  0.467   9.283  16826  Z= 0.238
  Chirality :  0.041   0.133   1818
  Planarity :  0.003   0.030   2144
  Dihedral  :  3.509  12.589   1662
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.56 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.22), residues: 1486
  helix:  1.53 (0.22), residues: 634
  sheet: -0.15 (0.38), residues: 198
  loop : -1.39 (0.23), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.006   0.001   HIS A 650 
 PHE   0.013   0.001   PHE B 649 
 TYR   0.009   0.001   TYR A 555 
 ARG   0.003   0.000   ARG B 578 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03064 (  465)
  hydrogen bonds       : angle       3.84654 ( 1338)
  covalent geometry    : bond        0.00248 (12458)
  covalent geometry    : angle       0.46706 (16826)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6693.52 seconds
wall clock time: 116 minutes 25.81 seconds (6985.81 seconds total)