Starting phenix.real_space_refine
on Mon Aug 25 05:26:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kgm_37226/08_2025/8kgm_37226.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kgm_37226/08_2025/8kgm_37226.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kgm_37226/08_2025/8kgm_37226.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kgm_37226/08_2025/8kgm_37226.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kgm_37226/08_2025/8kgm_37226.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kgm_37226/08_2025/8kgm_37226.cif"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6198 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      76      5.49       5
     S      96      5.16       5
     C   12879      2.51       5
     N    3519      2.21       5
     O    3924      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 20494
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1181, 9447
          Classifications: {'peptide': 1181}
          Link IDs: {'PCIS': 3, 'PTRANS': 44, 'TRANS': 1133}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 9490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1186, 9490
          Classifications: {'peptide': 1186}
          Link IDs: {'PCIS': 3, 'PTRANS': 44, 'TRANS': 1138}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 781
          Classifications: {'DNA': 38}
          Link IDs: {'rna3p': 37}
    Chain: "D"
      Number of atoms: 776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 776
          Classifications: {'DNA': 38}
          Link IDs: {'rna3p': 37}
  Time building chain proxies: 4.71, per 1000 atoms: 0.23
  Number of scatterers: 20494
  At special positions: 0
  Unit cell: (132.84, 127.1, 184.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      96     16.00
     P      76     15.00
     O    3924      8.00
     N    3519      7.00
     C   12879      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.61
  Conformation dependent library (CDL) restraints added in 965.0 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4462

  Finding SS restraints...
    Secondary structure from input PDB file:
      98 helices and 30 sheets defined
      46.9% alpha, 14.2% beta
      18 base pairs and 61 stacking pairs defined.
    Time for finding SS restraints: 2.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 16
    Processing helix  chain 'A' and resid 51 through 73
      removed outlier: 3.706A  pdb=" N   PHE A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ILE A  61 " --> pdb=" O   ILE A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 113
    Processing helix  chain 'A' and resid 117 through 125
    Processing helix  chain 'A' and resid 146 through 154
    Processing helix  chain 'A' and resid 211 through 233
    Processing helix  chain 'A' and resid 250 through 260
    Processing helix  chain 'A' and resid 279 through 283
    Processing helix  chain 'A' and resid 312 through 334
      removed outlier: 3.744A  pdb=" N   THR A 316 " --> pdb=" O   GLY A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 348
    Processing helix  chain 'A' and resid 375 through 381
    Processing helix  chain 'A' and resid 385 through 403
    Processing helix  chain 'A' and resid 440 through 450
    Processing helix  chain 'A' and resid 496 through 501
    Processing helix  chain 'A' and resid 502 through 512
    Processing helix  chain 'A' and resid 541 through 546
    Processing helix  chain 'A' and resid 546 through 560
    Processing helix  chain 'A' and resid 560 through 567
      removed outlier: 4.058A  pdb=" N   ILE A 564 " --> pdb=" O   TRP A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 602
      removed outlier: 3.721A  pdb=" N   LYS A 602 " --> pdb=" O   ALA A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 620
      removed outlier: 3.759A  pdb=" N   ALA A 619 " --> pdb=" O   GLY A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 630
      removed outlier: 4.413A  pdb=" N   SER A 627 " --> pdb=" O   HIS A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 636
      removed outlier: 3.948A  pdb=" N   VAL A 636 " --> pdb=" O   ASP A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 644
      No H-bonds generated for 'chain 'A' and resid 642 through 644'
    Processing helix  chain 'A' and resid 645 through 654
    Processing helix  chain 'A' and resid 657 through 665
    Processing helix  chain 'A' and resid 672 through 683
    Processing helix  chain 'A' and resid 687 through 692
    Processing helix  chain 'A' and resid 693 through 707
    Processing helix  chain 'A' and resid 715 through 729
    Processing helix  chain 'A' and resid 738 through 749
      removed outlier: 3.501A  pdb=" N   MET A 749 " --> pdb=" O   VAL A 745 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 755 through 765
    Processing helix  chain 'A' and resid 787 through 791
      removed outlier: 3.912A  pdb=" N   LEU A 790 " --> pdb=" O   SER A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 806 through 814
    Processing helix  chain 'A' and resid 815 through 819
    Processing helix  chain 'A' and resid 842 through 846
      removed outlier: 3.566A  pdb=" N   MET A 846 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 864 through 877
      removed outlier: 3.653A  pdb=" N   ILE A 868 " --> pdb=" O   GLN A 864 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 883 through 893
    Processing helix  chain 'A' and resid 942 through 953
      removed outlier: 3.788A  pdb=" N   SER A 953 " --> pdb=" O   SER A 949 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 through 958
      removed outlier: 3.818A  pdb=" N   THR A 958 " --> pdb=" O   SER A 954 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 990
      removed outlier: 4.360A  pdb=" N   VAL A 987 " --> pdb=" O   LEU A 983 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   GLU A 988 " --> pdb=" O   ASN A 984 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLU A 989 " --> pdb=" O   ARG A 985 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1003
    Processing helix  chain 'A' and resid 1027 through 1075
      removed outlier: 3.731A  pdb=" N   ILE A1031 " --> pdb=" O   THR A1027 " (cutoff:3.500A)
      Proline residue:  A1037  - end of helix
      removed outlier: 4.061A  pdb=" N   ALA A1063 " --> pdb=" O   ILE A1059 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE A1064 " --> pdb=" O   MET A1060 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   ARG A1066 " --> pdb=" O   THR A1062 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   ALA A1072 " --> pdb=" O   ILE A1068 " (cutoff:3.500A)
      removed outlier: 5.688A  pdb=" N   GLU A1073 " --> pdb=" O   ASN A1069 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1079
      removed outlier: 3.507A  pdb=" N   TYR A1079 " --> pdb=" O   LEU A1076 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1076 through 1079'
    Processing helix  chain 'A' and resid 1081 through 1091
    Processing helix  chain 'A' and resid 1098 through 1104
    Processing helix  chain 'A' and resid 1109 through 1116
    Processing helix  chain 'A' and resid 1122 through 1127
    Processing helix  chain 'A' and resid 1129 through 1133
      removed outlier: 3.691A  pdb=" N   LEU A1133 " --> pdb=" O   ALA A1130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1134 through 1159
    Processing helix  chain 'A' and resid 1168 through 1187
    Processing helix  chain 'B' and resid 8 through 16
    Processing helix  chain 'B' and resid 51 through 73
      removed outlier: 3.707A  pdb=" N   PHE B  58 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ILE B  61 " --> pdb=" O   ILE B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 113
    Processing helix  chain 'B' and resid 117 through 125
    Processing helix  chain 'B' and resid 146 through 154
    Processing helix  chain 'B' and resid 211 through 233
    Processing helix  chain 'B' and resid 250 through 260
    Processing helix  chain 'B' and resid 279 through 283
    Processing helix  chain 'B' and resid 312 through 334
      removed outlier: 3.745A  pdb=" N   THR B 316 " --> pdb=" O   GLY B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 348
    Processing helix  chain 'B' and resid 375 through 381
    Processing helix  chain 'B' and resid 385 through 405
    Processing helix  chain 'B' and resid 428 through 431
    Processing helix  chain 'B' and resid 440 through 450
    Processing helix  chain 'B' and resid 496 through 501
    Processing helix  chain 'B' and resid 502 through 513
    Processing helix  chain 'B' and resid 541 through 560
      removed outlier: 4.252A  pdb=" N   ILE B 548 " --> pdb=" O   GLY B 544 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   LEU B 549 " --> pdb=" O   CYS B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 566
      removed outlier: 3.987A  pdb=" N   ILE B 564 " --> pdb=" O   TRP B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 592 through 603
      removed outlier: 3.600A  pdb=" N   LYS B 602 " --> pdb=" O   ALA B 598 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLN B 603 " --> pdb=" O   TRP B 599 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 616 through 620
      removed outlier: 3.615A  pdb=" N   HIS B 620 " --> pdb=" O   LEU B 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 621 through 630
    Processing helix  chain 'B' and resid 632 through 636
      removed outlier: 3.944A  pdb=" N   VAL B 636 " --> pdb=" O   ASP B 633 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 644 through 654
      removed outlier: 3.899A  pdb=" N   LEU B 648 " --> pdb=" O   SER B 644 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   PHE B 653 " --> pdb=" O   PHE B 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 657 through 664
    Processing helix  chain 'B' and resid 672 through 683
    Processing helix  chain 'B' and resid 687 through 692
    Processing helix  chain 'B' and resid 693 through 707
    Processing helix  chain 'B' and resid 715 through 729
    Processing helix  chain 'B' and resid 738 through 749
      removed outlier: 3.633A  pdb=" N   MET B 749 " --> pdb=" O   VAL B 745 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 754 through 767
      removed outlier: 3.997A  pdb=" N   LEU B 758 " --> pdb=" O   GLY B 754 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 806 through 814
    Processing helix  chain 'B' and resid 815 through 819
    Processing helix  chain 'B' and resid 842 through 846
    Processing helix  chain 'B' and resid 864 through 877
      removed outlier: 3.616A  pdb=" N   ILE B 868 " --> pdb=" O   GLN B 864 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 882 through 893
      removed outlier: 3.659A  pdb=" N   LEU B 886 " --> pdb=" O   LYS B 882 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 942 through 951
    Processing helix  chain 'B' and resid 953 through 958
      removed outlier: 3.514A  pdb=" N   THR B 958 " --> pdb=" O   SER B 954 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 982 through 990
    Processing helix  chain 'B' and resid 997 through 1003
    Processing helix  chain 'B' and resid 1027 through 1075
      removed outlier: 3.717A  pdb=" N   ILE B1031 " --> pdb=" O   THR B1027 " (cutoff:3.500A)
      Proline residue:  B1037  - end of helix
      removed outlier: 4.021A  pdb=" N   ALA B1063 " --> pdb=" O   ILE B1059 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ILE B1064 " --> pdb=" O   MET B1060 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   ARG B1066 " --> pdb=" O   THR B1062 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   ALA B1072 " --> pdb=" O   ILE B1068 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   GLU B1073 " --> pdb=" O   ASN B1069 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1076 through 1079
    Processing helix  chain 'B' and resid 1081 through 1091
    Processing helix  chain 'B' and resid 1098 through 1103
    Processing helix  chain 'B' and resid 1109 through 1117
      removed outlier: 3.966A  pdb=" N   LYS B1116 " --> pdb=" O   GLU B1112 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ALA B1117 " --> pdb=" O   LEU B1113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1122 through 1127
    Processing helix  chain 'B' and resid 1129 through 1133
      removed outlier: 3.500A  pdb=" N   LEU B1133 " --> pdb=" O   ALA B1130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1134 through 1159
    Processing helix  chain 'B' and resid 1166 through 1187
      removed outlier: 3.972A  pdb=" N   TRP B1170 " --> pdb=" O   GLY B1166 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU B1171 " --> pdb=" O   ALA B1167 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   THR B1187 " --> pdb=" O   LYS B1183 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6
    Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 36
    Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 180
    Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 180
      removed outlier: 5.330A  pdb=" N   GLN A 167 " --> pdb=" O   ASP A 164 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   TRP A 157 " --> pdb=" O   MET A 198 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ILE A  82 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129
    Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 304
      removed outlier: 3.889A  pdb=" N   LYS A 274 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 362 through 363
    Processing sheet with id=AA8, first strand: chain 'A' and resid 465 through 469
      removed outlier: 3.789A  pdb=" N   ILE A 468 " --> pdb=" O   LEU A 435 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   LEU A 434 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   CYS A 537 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ALA A 436 " --> pdb=" O   CYS A 537 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   VAL A 569 " --> pdb=" O   PHE A 639 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 481 through 484
    Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590
    Processing sheet with id=AB2, first strand: chain 'A' and resid 736 through 737
    Processing sheet with id=AB3, first strand: chain 'A' and resid 824 through 827
      removed outlier: 3.667A  pdb=" N   GLU A 833 " --> pdb=" O   VAL A 825 " (cutoff:3.500A)
      removed outlier: 5.701A  pdb=" N   GLU A 827 " --> pdb=" O   ARG A 831 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   ARG A 831 " --> pdb=" O   GLU A 827 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 849 through 852
      removed outlier: 3.545A  pdb=" N   GLY A 849 " --> pdb=" O   THR A 860 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 909 through 912
      removed outlier: 3.722A  pdb=" N   HIS A 909 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   TYR A 917 " --> pdb=" O   LEU A1009 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 933 through 934
      removed outlier: 3.727A  pdb=" N   GLU A 962 " --> pdb=" O   LYS A 977 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1014 through 1016
    Processing sheet with id=AB8, first strand: chain 'B' and resid 32 through 36
    Processing sheet with id=AB9, first strand: chain 'B' and resid 179 through 180
    Processing sheet with id=AC1, first strand: chain 'B' and resid 179 through 180
      removed outlier: 5.330A  pdb=" N   GLN B 167 " --> pdb=" O   ASP B 164 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   TRP B 157 " --> pdb=" O   MET B 198 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ILE B  82 " --> pdb=" O   TYR B 240 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 299 through 304
      removed outlier: 3.889A  pdb=" N   LYS B 274 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 362 through 363
    Processing sheet with id=AC4, first strand: chain 'B' and resid 418 through 419
      removed outlier: 3.710A  pdb=" N   ILE B 468 " --> pdb=" O   LEU B 435 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   LEU B 434 " --> pdb=" O   VAL B 535 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   CYS B 537 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   ALA B 436 " --> pdb=" O   CYS B 537 " (cutoff:3.500A)
      removed outlier: 5.782A  pdb=" N   VAL B 569 " --> pdb=" O   PHE B 639 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 481 through 485
    Processing sheet with id=AC6, first strand: chain 'B' and resid 588 through 590
    Processing sheet with id=AC7, first strand: chain 'B' and resid 736 through 737
      removed outlier: 3.694A  pdb=" N   ARG B 736 " --> pdb=" O   VAL B 803 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 824 through 827
      removed outlier: 3.771A  pdb=" N   GLU B 833 " --> pdb=" O   VAL B 825 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   GLU B 827 " --> pdb=" O   ARG B 831 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   ARG B 831 " --> pdb=" O   GLU B 827 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 849 through 852
      removed outlier: 3.652A  pdb=" N   GLY B 849 " --> pdb=" O   THR B 860 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 909 through 913
      removed outlier: 3.514A  pdb=" N   TYR B 916 " --> pdb=" O   PHE B 913 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 925 through 926
      removed outlier: 4.202A  pdb=" N   ILE B 932 " --> pdb=" O   VAL B 976 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLU B 962 " --> pdb=" O   LYS B 977 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 1014 through 1016

    895 hydrogen bonds defined for protein.
    2523 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      40 hydrogen bonds
      72 hydrogen bond angles
      0 basepair planarities
      18 basepair parallelities
      61 stacking parallelities
  Total time for adding SS restraints: 5.28

  Time building geometry restraints manager: 2.21 seconds

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

  Histogram of bond lengths:
        1.20 -     1.34: 5987
        1.34 -     1.47: 5888
        1.47 -     1.60: 9060
        1.60 -     1.74: 24
        1.74 -     1.87: 148
  Bond restraints: 21107
  Sorted by residual:
  bond pdb=" CD  GLU A 106 "
       pdb=" OE2 GLU A 106 "
    ideal  model  delta    sigma   weight residual
    1.249  1.329 -0.080 1.90e-02 2.77e+03 1.79e+01
  bond pdb=" CD  GLU B 106 "
       pdb=" OE2 GLU B 106 "
    ideal  model  delta    sigma   weight residual
    1.249  1.329 -0.080 1.90e-02 2.77e+03 1.78e+01
  bond pdb=" CA  ARG B 344 "
       pdb=" C   ARG B 344 "
    ideal  model  delta    sigma   weight residual
    1.523  1.483  0.040 1.37e-02 5.33e+03 8.60e+00
  bond pdb=" CA  ARG A 344 "
       pdb=" C   ARG A 344 "
    ideal  model  delta    sigma   weight residual
    1.523  1.483  0.040 1.37e-02 5.33e+03 8.34e+00
  bond pdb=" CA  PHE B   4 "
       pdb=" C   PHE B   4 "
    ideal  model  delta    sigma   weight residual
    1.524  1.491  0.033 1.23e-02 6.61e+03 7.22e+00
  ... (remaining 21102 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.24: 28494
        3.24 -     6.48: 333
        6.48 -     9.73: 31
        9.73 -    12.97: 2
       12.97 -    16.21: 3
  Bond angle restraints: 28863
  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
     121.54  130.53   -8.99 1.91e+00 2.74e-01 2.22e+01
  angle pdb=" N   ARG A 344 "
        pdb=" CA  ARG A 344 "
        pdb=" C   ARG A 344 "
      ideal   model   delta    sigma   weight residual
     112.23  106.46    5.77 1.26e+00 6.30e-01 2.10e+01
  angle pdb=" N   ARG B 344 "
        pdb=" CA  ARG B 344 "
        pdb=" C   ARG B 344 "
      ideal   model   delta    sigma   weight residual
     112.23  106.49    5.74 1.26e+00 6.30e-01 2.08e+01
  angle pdb=" N   ASP B 408 "
        pdb=" CA  ASP B 408 "
        pdb=" C   ASP B 408 "
      ideal   model   delta    sigma   weight residual
     112.92  107.49    5.43 1.23e+00 6.61e-01 1.95e+01
  angle pdb=" CA  LEU A 261 "
        pdb=" CB  LEU A 261 "
        pdb=" CG  LEU A 261 "
      ideal   model   delta    sigma   weight residual
     116.30  101.05   15.25 3.50e+00 8.16e-02 1.90e+01
  ... (remaining 28858 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.65: 12099
       35.65 -    71.29: 454
       71.29 -   106.93: 14
      106.93 -   142.58: 1
      142.58 -   178.22: 3
  Dihedral angle restraints: 12571
    sinusoidal: 5638
      harmonic: 6933
  Sorted by residual:
  dihedral pdb=" CA  ARG A 247 "
           pdb=" C   ARG A 247 "
           pdb=" N   THR A 248 "
           pdb=" CA  THR A 248 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.97  -28.03     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  ARG B 247 "
           pdb=" C   ARG B 247 "
           pdb=" N   THR B 248 "
           pdb=" CA  THR B 248 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.00  -28.00     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  THR A1062 "
           pdb=" C   THR A1062 "
           pdb=" N   ALA A1063 "
           pdb=" CA  ALA A1063 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.36   26.64     0      5.00e+00 4.00e-02 2.84e+01
  ... (remaining 12568 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 2626
       0.075 -    0.151: 538
       0.151 -    0.226: 42
       0.226 -    0.301: 6
       0.301 -    0.377: 3
  Chirality restraints: 3215
  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    0.38 2.00e-01 2.50e+01 3.55e+00
  chirality pdb=" CB  ILE B 963 "
            pdb=" CA  ILE B 963 "
            pdb=" CG1 ILE B 963 "
            pdb=" CG2 ILE B 963 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.47e+00
  chirality pdb=" C3'  DT C  44 "
            pdb=" C4'  DT C  44 "
            pdb=" O3'  DT C  44 "
            pdb=" C2'  DT C  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.35   -0.31 2.00e-01 2.50e+01 2.44e+00
  ... (remaining 3212 not shown)

  Planarity restraints: 3397
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B1170 "   -0.026 2.00e-02 2.50e+03   2.66e-02 1.77e+01
        pdb=" CG  TRP B1170 "    0.071 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 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B1170 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B1170 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B1170 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B1170 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B1170 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1170 "   -0.025 2.00e-02 2.50e+03   2.60e-02 1.69e+01
        pdb=" CG  TRP A1170 "    0.069 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1170 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1170 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1170 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1170 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1170 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1170 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1170 "   -0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1170 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 531 "    0.037 2.00e-02 2.50e+03   2.57e-02 1.32e+01
        pdb=" CG  TYR A 531 "   -0.060 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 531 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 531 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 531 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 531 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 531 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 531 "    0.007 2.00e-02 2.50e+03
  ... (remaining 3394 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 20
        2.18 -     2.86: 6930
        2.86 -     3.54: 26878
        3.54 -     4.22: 49374
        4.22 -     4.90: 83515
  Nonbonded interactions: 166717
  Sorted by model distance:
  nonbonded pdb=" N   GLY A 855 "
            pdb=" OP1  DA C  39 "
     model   vdw
     1.497 3.120
  nonbonded pdb=" NH1 ARG A 344 "
            pdb=" NH1 ARG B 344 "
     model   vdw
     1.624 3.200
  nonbonded pdb=" OD1 ASN A 851 "
            pdb=" O4'  DG D  15 "
     model   vdw
     1.698 3.040
  nonbonded pdb=" OE2 GLU A 854 "
            pdb=" C5'  DC C  38 "
     model   vdw
     1.822 3.440
  nonbonded pdb=" O   TRP A 856 "
            pdb=" C4'  DA C  39 "
     model   vdw
     1.883 3.470
  ... (remaining 166712 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 3 through 403 or resid 414 through 1192))
  selection = (chain 'B' and (resid 3 through 403 or resid 408 or resid 415 through 1192))
}
ncs_group {
  reference = (chain 'C' and (resid 14 through 18 or resid 20 through 22 or resid 24 through 3 \ 
9 or resid 41 through 43 or resid 45 through 49 or resid 51))
  selection = (chain 'D' and (resid 4 through 8 or resid 10 through 12 or resid 14 through 29  \ 
or resid 31 through 33 or resid 35 through 39 or resid 41))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     22.750
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4648
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      :  0.008   0.080  21107  Z= 0.374
  Angle     :  0.982  16.211  28863  Z= 0.544
  Chirality :  0.059   0.377   3215
  Planarity :  0.007   0.077   3397
  Dihedral  : 16.569 178.224   8109
  Min Nonbonded Distance : 1.497

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.69 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  7.50 %
    Favored  : 91.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.85 (0.15), residues: 2359
  helix: -1.95 (0.13), residues: 972
  sheet: -1.25 (0.28), residues: 349
  loop : -1.91 (0.17), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.002   ARG B1039 
 TYR   0.060   0.003   TYR A 531 
 PHE   0.026   0.003   PHE B 739 
 TRP   0.071   0.004   TRP B1170 
 HIS   0.014   0.003   HIS B 892 

Details of bonding type rmsd
  covalent geometry    : bond        0.00836 (21107)
  covalent geometry    : angle       0.98192 (28863)
  hydrogen bonds       : bond        0.16766 (  931)
  hydrogen bonds       : angle       7.03496 ( 2595)

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

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

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  462 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 448
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 LEU cc_start: 0.8471 (tp) cc_final: 0.8257 (tp)
REVERT: A  576 LEU cc_start: 0.7165 (tp) cc_final: 0.6890 (tp)
REVERT: A  721 ILE cc_start: 0.9196 (mt) cc_final: 0.8747 (mt)
REVERT: A  722 LEU cc_start: 0.9204 (tp) cc_final: 0.8975 (tp)
REVERT: A  776 TYR cc_start: 0.7521 (m-80) cc_final: 0.7292 (m-80)
REVERT: A  836 TYR cc_start: 0.6422 (p90) cc_final: 0.6221 (p90)
REVERT: A  838 VAL cc_start: 0.8600 (t) cc_final: 0.8110 (p)
REVERT: A  848 TYR cc_start: 0.5381 (m-80) cc_final: 0.5100 (m-10)
REVERT: B  392 MET cc_start: 0.0463 (mmm) cc_final: 0.0234 (mmm)
REVERT: B  446 LEU cc_start: 0.8713 (mt) cc_final: 0.8383 (mt)
REVERT: B  541 ASP cc_start: 0.7602 (p0) cc_final: 0.7141 (p0)
REVERT: B  573 LEU cc_start: 0.7945 (tm) cc_final: 0.7643 (tm)
REVERT: B  621 ASP cc_start: 0.8433 (t0) cc_final: 0.8228 (t70)
REVERT: B  722 LEU cc_start: 0.9066 (tp) cc_final: 0.8834 (tp)
REVERT: B  939 LEU cc_start: 0.8310 (mt) cc_final: 0.7883 (mt)
REVERT: B 1181 ILE cc_start: 0.8715 (mt) cc_final: 0.8458 (mm)
  outliers start: 14
  outliers final: 1
  residues processed: 462
  average time/residue: 0.1683
  time to fit residues: 114.2299
Evaluate side-chains
  246 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 245
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 216 optimal weight:    2.9990
   chunk 98 optimal weight:    7.9990
   chunk 194 optimal weight:    4.9990
   chunk 227 optimal weight:    0.4980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:   40.0000
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9980
   chunk 235 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
A 283 HIS
A 323 ASN
A 566 HIS
A 677 GLN
A 883 HIS
** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 HIS
B 175 GLN
B 283 HIS
B 483 ASN
** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 562 GLN
B 566 HIS
B 692 GLN
B 748 HIS
** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 864 GLN
B 892 HIS
B 905 ASN
B1069 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.078994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.051784 restraints weight = 168618.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.053622 restraints weight = 109466.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.054812 restraints weight = 78857.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.055329 restraints weight = 60842.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.056476 restraints weight = 50666.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  21107  Z= 0.155
  Angle     :  0.644  14.209  28863  Z= 0.350
  Chirality :  0.044   0.211   3215
  Planarity :  0.005   0.046   3397
  Dihedral  : 17.512 174.276   3463
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.52 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.20 (0.16), residues: 2359
  helix: -0.23 (0.16), residues: 983
  sheet: -0.53 (0.28), residues: 338
  loop : -1.36 (0.18), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 571 
 TYR   0.023   0.002   TYR A 698 
 PHE   0.028   0.002   PHE B 317 
 TRP   0.026   0.001   TRP B1170 
 HIS   0.007   0.001   HIS B 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (21107)
  covalent geometry    : angle       0.64373 (28863)
  hydrogen bonds       : bond        0.05856 (  931)
  hydrogen bonds       : angle       5.26223 ( 2595)

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

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

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 283
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 MET cc_start: -0.5935 (mmm) cc_final: -0.6311 (mmm)
REVERT: A  629 PHE cc_start: 0.9585 (m-10) cc_final: 0.9332 (m-10)
REVERT: A  698 TYR cc_start: 0.9454 (t80) cc_final: 0.8617 (t80)
REVERT: A  737 LYS cc_start: 0.8774 (tppt) cc_final: 0.8511 (tppp)
REVERT: A  739 PHE cc_start: 0.9393 (p90) cc_final: 0.9114 (p90)
REVERT: A  760 THR cc_start: 0.9668 (m) cc_final: 0.9454 (p)
REVERT: A  775 LEU cc_start: 0.9297 (tp) cc_final: 0.8901 (tp)
REVERT: A  776 TYR cc_start: 0.9207 (m-80) cc_final: 0.8988 (m-80)
REVERT: A  843 LEU cc_start: 0.9580 (mt) cc_final: 0.9367 (mm)
REVERT: A  846 MET cc_start: 0.9604 (mtp) cc_final: 0.9352 (mtt)
REVERT: A  854 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8486 (tp30)
REVERT: A  957 MET cc_start: 0.9132 (mmp) cc_final: 0.8786 (mmm)
REVERT: A  962 GLU cc_start: 0.8440 (tp30) cc_final: 0.8104 (tp30)
REVERT: A  988 GLU cc_start: 0.9089 (mp0) cc_final: 0.8466 (pm20)
REVERT: A 1078 HIS cc_start: 0.9600 (t70) cc_final: 0.9374 (t70)
REVERT: A 1129 GLN cc_start: 0.9250 (mt0) cc_final: 0.9046 (mt0)
REVERT: B   18 MET cc_start: -0.0187 (ptt) cc_final: -0.1851 (mmt)
REVERT: B  447 ARG cc_start: 0.9336 (mtm-85) cc_final: 0.9056 (ptp90)
REVERT: B  502 ASN cc_start: 0.8850 (t0) cc_final: 0.8573 (t0)
REVERT: B  573 LEU cc_start: 0.8764 (tt) cc_final: 0.8519 (tp)
REVERT: B  586 MET cc_start: 0.8256 (mmm) cc_final: 0.7937 (mmm)
REVERT: B  606 LEU cc_start: 0.8565 (tp) cc_final: 0.8277 (mm)
REVERT: B  621 ASP cc_start: 0.9694 (t0) cc_final: 0.9447 (t70)
REVERT: B  628 MET cc_start: 0.9355 (mtm) cc_final: 0.9128 (mtt)
REVERT: B  714 MET cc_start: 0.8692 (ppp) cc_final: 0.8408 (tmm)
REVERT: B  790 LEU cc_start: 0.9405 (mp) cc_final: 0.8937 (tp)
REVERT: B  813 MET cc_start: 0.9523 (tpt) cc_final: 0.8690 (tpp)
REVERT: B  846 MET cc_start: 0.9217 (mtm) cc_final: 0.8856 (mtp)
REVERT: B  939 LEU cc_start: 0.9420 (mt) cc_final: 0.9127 (mt)
REVERT: B  962 GLU cc_start: 0.9225 (tt0) cc_final: 0.9014 (tm-30)
REVERT: B  966 TYR cc_start: 0.9059 (m-80) cc_final: 0.8739 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 285
  average time/residue: 0.1601
  time to fit residues: 68.6223
Evaluate side-chains
  213 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 189 optimal weight:    4.9990
   chunk 154 optimal weight:   20.0000
   chunk 66 optimal weight:    0.5980
   chunk 179 optimal weight:    7.9990
   chunk 241 optimal weight:    6.9990
   chunk 186 optimal weight:    8.9990
   chunk 2 optimal weight:   30.0000
   chunk 149 optimal weight:    9.9990
   chunk 228 optimal weight:    6.9990
   chunk 115 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    5.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 506 GLN
** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 864 GLN
** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1099 HIS
A1149 GLN
** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 286 GLN
** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 692 GLN
** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.068914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.043243 restraints weight = 181186.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.044678 restraints weight = 119210.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.045768 restraints weight = 87669.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.046146 restraints weight = 68981.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.047084 restraints weight = 58477.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.4617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078  21107  Z= 0.268
  Angle     :  0.745  12.894  28863  Z= 0.399
  Chirality :  0.046   0.289   3215
  Planarity :  0.005   0.067   3397
  Dihedral  : 17.598 175.549   3463
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 17.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  3.97 %
    Favored  : 95.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.17), residues: 2359
  helix:  0.43 (0.16), residues: 985
  sheet: -0.70 (0.27), residues: 388
  loop : -0.78 (0.20), residues: 986

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 571 
 TYR   0.024   0.002   TYR B 837 
 PHE   0.035   0.003   PHE B 785 
 TRP   0.018   0.002   TRP A1170 
 HIS   0.011   0.002   HIS A 892 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 (21107)
  covalent geometry    : angle       0.74529 (28863)
  hydrogen bonds       : bond        0.05792 (  931)
  hydrogen bonds       : angle       5.31174 ( 2595)

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

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

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 219
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 MET cc_start: 0.3284 (ptm) cc_final: 0.2763 (ptm)
REVERT: A  392 MET cc_start: -0.5658 (mmm) cc_final: -0.6041 (mmm)
REVERT: A  446 LEU cc_start: 0.9740 (mt) cc_final: 0.9457 (mt)
REVERT: A  467 MET cc_start: 0.9180 (mtp) cc_final: 0.8788 (mtp)
REVERT: A  474 ILE cc_start: 0.9131 (mp) cc_final: 0.8925 (pt)
REVERT: A  475 MET cc_start: 0.7511 (mmp) cc_final: 0.6961 (tpp)
REVERT: A  586 MET cc_start: 0.9015 (mmp) cc_final: 0.8613 (tpp)
REVERT: A  684 ARG cc_start: 0.9706 (mtm180) cc_final: 0.9445 (mmm-85)
REVERT: A  698 TYR cc_start: 0.9548 (t80) cc_final: 0.8582 (t80)
REVERT: A  704 GLU cc_start: 0.9562 (tp30) cc_final: 0.9157 (tp30)
REVERT: A  714 MET cc_start: 0.9568 (ttt) cc_final: 0.9005 (ttp)
REVERT: A  775 LEU cc_start: 0.9496 (tp) cc_final: 0.9293 (tp)
REVERT: A  846 MET cc_start: 0.9628 (mtp) cc_final: 0.9317 (mtt)
REVERT: A  854 GLU cc_start: 0.9471 (mm-30) cc_final: 0.9120 (mm-30)
REVERT: A  957 MET cc_start: 0.9175 (mmp) cc_final: 0.8782 (mmm)
REVERT: A  962 GLU cc_start: 0.8667 (tp30) cc_final: 0.8183 (tp30)
REVERT: A 1042 LEU cc_start: 0.9536 (mt) cc_final: 0.9321 (mt)
REVERT: B   18 MET cc_start: 0.1039 (ptt) cc_final: 0.0734 (ppp)
REVERT: B   32 MET cc_start: 0.4554 (tpt) cc_final: 0.3752 (ptt)
REVERT: B  257 MET cc_start: -0.0627 (tmm) cc_final: -0.0933 (tmm)
REVERT: B  573 LEU cc_start: 0.8863 (tt) cc_final: 0.8605 (pp)
REVERT: B  576 LEU cc_start: 0.9077 (tp) cc_final: 0.8691 (tp)
REVERT: B  586 MET cc_start: 0.8523 (mmm) cc_final: 0.8199 (mmm)
REVERT: B  621 ASP cc_start: 0.9707 (t0) cc_final: 0.9428 (t70)
REVERT: B  755 ASP cc_start: 0.9655 (p0) cc_final: 0.9280 (p0)
REVERT: B  790 LEU cc_start: 0.9450 (mp) cc_final: 0.9118 (tt)
REVERT: B  813 MET cc_start: 0.9556 (tpt) cc_final: 0.8582 (tpp)
REVERT: B  828 ASP cc_start: 0.9240 (m-30) cc_final: 0.8497 (t0)
REVERT: B  838 VAL cc_start: 0.9511 (t) cc_final: 0.9206 (p)
REVERT: B  846 MET cc_start: 0.9363 (mtm) cc_final: 0.8894 (mtp)
REVERT: B  962 GLU cc_start: 0.9354 (tt0) cc_final: 0.9112 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 220
  average time/residue: 0.1523
  time to fit residues: 51.8408
Evaluate side-chains
  165 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 164
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 123 optimal weight:   30.0000
   chunk 48 optimal weight:    5.9990
   chunk 187 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0270
   chunk 176 optimal weight:    0.7980
   chunk 69 optimal weight:   10.0000
   chunk 237 optimal weight:    6.9990
   chunk 112 optimal weight:    0.7980
   chunk 110 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 228 optimal weight:    8.9990
   overall best weight:    0.7240

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

Flipped N/Q/H residues before XYZ refinement:
A 381 HIS
** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 883 HIS
** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 172 HIS
B 175 GLN
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 692 GLN
B 905 ASN
** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.072265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.045829 restraints weight = 173347.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.047348 restraints weight = 110992.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.048643 restraints weight = 79626.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.049049 restraints weight = 61355.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.050087 restraints weight = 51583.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.4637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  21107  Z= 0.125
  Angle     :  0.598  11.397  28863  Z= 0.316
  Chirality :  0.043   0.267   3215
  Planarity :  0.004   0.098   3397
  Dihedral  : 17.393 172.907   3463
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.23 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.18), residues: 2359
  helix:  0.84 (0.17), residues: 988
  sheet: -0.56 (0.27), residues: 382
  loop : -0.63 (0.20), residues: 989

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 683 
 TYR   0.017   0.001   TYR B 837 
 PHE   0.017   0.001   PHE B 388 
 TRP   0.011   0.001   TRP B1189 
 HIS   0.005   0.001   HIS B1051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (21107)
  covalent geometry    : angle       0.59756 (28863)
  hydrogen bonds       : bond        0.04725 (  931)
  hydrogen bonds       : angle       4.95368 ( 2595)

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

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

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 224
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.3253 (tmm) cc_final: 0.2404 (tmm)
REVERT: A  257 MET cc_start: 0.3250 (ptm) cc_final: 0.2840 (ptm)
REVERT: A  392 MET cc_start: -0.5536 (mmm) cc_final: -0.5741 (mmm)
REVERT: A  483 ASN cc_start: 0.8917 (p0) cc_final: 0.8516 (m-40)
REVERT: A  503 LYS cc_start: 0.9530 (ptmm) cc_final: 0.9251 (ptmm)
REVERT: A  586 MET cc_start: 0.8966 (mmp) cc_final: 0.8574 (tpp)
REVERT: A  684 ARG cc_start: 0.9670 (mtm180) cc_final: 0.9429 (mmm-85)
REVERT: A  698 TYR cc_start: 0.9478 (t80) cc_final: 0.8456 (t80)
REVERT: A  704 GLU cc_start: 0.9506 (tp30) cc_final: 0.9001 (tp30)
REVERT: A  775 LEU cc_start: 0.9506 (tp) cc_final: 0.8994 (tp)
REVERT: A  846 MET cc_start: 0.9724 (mtp) cc_final: 0.9194 (mtt)
REVERT: A  854 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8807 (mm-30)
REVERT: A  957 MET cc_start: 0.9229 (mmp) cc_final: 0.8831 (mmm)
REVERT: A  962 GLU cc_start: 0.8519 (tp30) cc_final: 0.8032 (tp30)
REVERT: B   18 MET cc_start: 0.0262 (ptt) cc_final: -0.1274 (mmt)
REVERT: B   32 MET cc_start: 0.3808 (tpt) cc_final: 0.3539 (tpt)
REVERT: B  502 ASN cc_start: 0.9098 (t0) cc_final: 0.8857 (t0)
REVERT: B  573 LEU cc_start: 0.8858 (tt) cc_final: 0.8471 (tp)
REVERT: B  576 LEU cc_start: 0.9006 (tp) cc_final: 0.8573 (tp)
REVERT: B  586 MET cc_start: 0.8573 (mmm) cc_final: 0.8226 (mmm)
REVERT: B  606 LEU cc_start: 0.8509 (tp) cc_final: 0.8182 (mm)
REVERT: B  621 ASP cc_start: 0.9730 (t0) cc_final: 0.9488 (t70)
REVERT: B  629 PHE cc_start: 0.9348 (m-10) cc_final: 0.9119 (m-10)
REVERT: B  698 TYR cc_start: 0.9574 (t80) cc_final: 0.9292 (t80)
REVERT: B  700 LEU cc_start: 0.9690 (mt) cc_final: 0.9485 (mt)
REVERT: B  813 MET cc_start: 0.9606 (tpt) cc_final: 0.8728 (tpp)
REVERT: B  828 ASP cc_start: 0.9083 (m-30) cc_final: 0.8379 (t0)
REVERT: B  838 VAL cc_start: 0.9380 (t) cc_final: 0.9061 (p)
REVERT: B  846 MET cc_start: 0.9362 (mtm) cc_final: 0.8783 (mtp)
REVERT: B  962 GLU cc_start: 0.9317 (tt0) cc_final: 0.9092 (tm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 226
  average time/residue: 0.1452
  time to fit residues: 52.3916
Evaluate side-chains
  181 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 150 optimal weight:    4.9990
   chunk 155 optimal weight:   50.0000
   chunk 93 optimal weight:    0.9980
   chunk 135 optimal weight:    7.9990
   chunk 195 optimal weight:    0.7980
   chunk 190 optimal weight:    8.9990
   chunk 139 optimal weight:   40.0000
   chunk 154 optimal weight:    0.0970
   chunk 148 optimal weight:    5.9990
   chunk 119 optimal weight:    6.9990
   chunk 106 optimal weight:   10.0000
   overall best weight:    2.5782

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

Flipped N/Q/H residues before XYZ refinement:
A 381 HIS
** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 892 HIS
** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 GLN
** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 692 GLN
B 759 ASN
** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.070236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.044193 restraints weight = 173674.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.045812 restraints weight = 114646.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.046379 restraints weight = 82950.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.047582 restraints weight = 67342.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.047941 restraints weight = 54884.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.5055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  21107  Z= 0.158
  Angle     :  0.627  28.299  28863  Z= 0.326
  Chirality :  0.045   0.620   3215
  Planarity :  0.004   0.053   3397
  Dihedral  : 17.337 173.027   3463
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  1.64 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.18), residues: 2359
  helix:  0.96 (0.17), residues: 990
  sheet: -0.50 (0.27), residues: 396
  loop : -0.46 (0.21), residues: 973

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 683 
 TYR   0.017   0.002   TYR B 837 
 PHE   0.020   0.002   PHE B 596 
 TRP   0.020   0.001   TRP A1170 
 HIS   0.012   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (21107)
  covalent geometry    : angle       0.62738 (28863)
  hydrogen bonds       : bond        0.04760 (  931)
  hydrogen bonds       : angle       4.94567 ( 2595)

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

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

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.3428 (tmm) cc_final: 0.2596 (tmm)
REVERT: A  257 MET cc_start: 0.3370 (ptm) cc_final: 0.2899 (ptm)
REVERT: A  446 LEU cc_start: 0.9809 (mt) cc_final: 0.9557 (mt)
REVERT: A  467 MET cc_start: 0.9300 (mtp) cc_final: 0.8866 (ttt)
REVERT: A  475 MET cc_start: 0.8030 (mmp) cc_final: 0.7111 (tpp)
REVERT: A  483 ASN cc_start: 0.8930 (p0) cc_final: 0.8532 (m-40)
REVERT: A  586 MET cc_start: 0.9011 (mmp) cc_final: 0.8623 (tpp)
REVERT: A  698 TYR cc_start: 0.9457 (t80) cc_final: 0.8425 (t80)
REVERT: A  704 GLU cc_start: 0.9541 (tp30) cc_final: 0.8999 (tp30)
REVERT: A  749 MET cc_start: 0.8880 (mmm) cc_final: 0.8541 (mmm)
REVERT: A  854 GLU cc_start: 0.9449 (mm-30) cc_final: 0.8704 (mm-30)
REVERT: A  957 MET cc_start: 0.9243 (mmp) cc_final: 0.8801 (mmm)
REVERT: A  962 GLU cc_start: 0.8610 (tp30) cc_final: 0.8108 (tp30)
REVERT: B   18 MET cc_start: 0.0525 (ptt) cc_final: -0.1161 (mmt)
REVERT: B   32 MET cc_start: 0.3459 (tpt) cc_final: 0.3013 (tpp)
REVERT: B  447 ARG cc_start: 0.9271 (mtm-85) cc_final: 0.8899 (mtt-85)
REVERT: B  502 ASN cc_start: 0.9086 (t0) cc_final: 0.8845 (t0)
REVERT: B  541 ASP cc_start: 0.8625 (p0) cc_final: 0.8257 (p0)
REVERT: B  573 LEU cc_start: 0.8853 (tt) cc_final: 0.8455 (tp)
REVERT: B  586 MET cc_start: 0.8505 (mmm) cc_final: 0.8187 (mmm)
REVERT: B  621 ASP cc_start: 0.9725 (t0) cc_final: 0.9472 (t70)
REVERT: B  700 LEU cc_start: 0.9713 (mt) cc_final: 0.9347 (mt)
REVERT: B  813 MET cc_start: 0.9609 (tpt) cc_final: 0.8710 (tpp)
REVERT: B  828 ASP cc_start: 0.9314 (m-30) cc_final: 0.8407 (t0)
REVERT: B  838 VAL cc_start: 0.9411 (t) cc_final: 0.9082 (p)
REVERT: B  846 MET cc_start: 0.9374 (mtm) cc_final: 0.8852 (mtp)
REVERT: B  957 MET cc_start: 0.8912 (mmp) cc_final: 0.8677 (mmm)
REVERT: B  962 GLU cc_start: 0.9317 (tt0) cc_final: 0.9094 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 210
  average time/residue: 0.1446
  time to fit residues: 48.1875
Evaluate side-chains
  168 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 195 optimal weight:    4.9990
   chunk 185 optimal weight:    0.9990
   chunk 151 optimal weight:   10.0000
   chunk 145 optimal weight:   20.0000
   chunk 176 optimal weight:    3.9990
   chunk 7 optimal weight:    0.1980
   chunk 203 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 189 optimal weight:    0.7980
   chunk 21 optimal weight:   40.0000
   chunk 127 optimal weight:   50.0000
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 105 HIS
A 381 HIS
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  47 HIS
** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 692 GLN
B 905 ASN
** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.069874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.043967 restraints weight = 174638.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.045385 restraints weight = 113613.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.046554 restraints weight = 82743.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.046949 restraints weight = 63652.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.047902 restraints weight = 53512.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.5345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  21107  Z= 0.141
  Angle     :  0.594  15.607  28863  Z= 0.314
  Chirality :  0.044   0.552   3215
  Planarity :  0.004   0.125   3397
  Dihedral  : 17.282 173.116   3463
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.18), residues: 2359
  helix:  1.04 (0.17), residues: 999
  sheet: -0.51 (0.27), residues: 395
  loop : -0.46 (0.21), residues: 965

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 831 
 TYR   0.024   0.001   TYR B 824 
 PHE   0.021   0.001   PHE B 596 
 TRP   0.013   0.001   TRP A1170 
 HIS   0.010   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (21107)
  covalent geometry    : angle       0.59425 (28863)
  hydrogen bonds       : bond        0.04470 (  931)
  hydrogen bonds       : angle       4.84659 ( 2595)

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

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

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.3508 (tmm) cc_final: 0.2702 (tmm)
REVERT: A  257 MET cc_start: 0.3242 (ptm) cc_final: 0.2770 (ptm)
REVERT: A  446 LEU cc_start: 0.9821 (mt) cc_final: 0.9594 (mt)
REVERT: A  467 MET cc_start: 0.9292 (mtp) cc_final: 0.8854 (ttt)
REVERT: A  475 MET cc_start: 0.8510 (mmp) cc_final: 0.7983 (tpp)
REVERT: A  483 ASN cc_start: 0.8906 (p0) cc_final: 0.8578 (m-40)
REVERT: A  493 MET cc_start: 0.9617 (tpp) cc_final: 0.9354 (tpp)
REVERT: A  586 MET cc_start: 0.8992 (mmp) cc_final: 0.8616 (tpp)
REVERT: A  698 TYR cc_start: 0.9448 (t80) cc_final: 0.8533 (t80)
REVERT: A  704 GLU cc_start: 0.9507 (tp30) cc_final: 0.8970 (tp30)
REVERT: A  749 MET cc_start: 0.8889 (mmm) cc_final: 0.8565 (mmm)
REVERT: A  764 LYS cc_start: 0.9673 (mtpt) cc_final: 0.9433 (mmmm)
REVERT: A  854 GLU cc_start: 0.9496 (mm-30) cc_final: 0.9086 (mm-30)
REVERT: A  957 MET cc_start: 0.9253 (mmp) cc_final: 0.8814 (mmm)
REVERT: A  962 GLU cc_start: 0.8564 (tp30) cc_final: 0.8047 (tp30)
REVERT: A 1042 LEU cc_start: 0.9518 (mt) cc_final: 0.9265 (mt)
REVERT: B   18 MET cc_start: 0.0523 (ptt) cc_final: -0.1180 (mmt)
REVERT: B  447 ARG cc_start: 0.9240 (mtm-85) cc_final: 0.8844 (mtt-85)
REVERT: B  573 LEU cc_start: 0.8826 (tt) cc_final: 0.8446 (tp)
REVERT: B  586 MET cc_start: 0.8523 (mmm) cc_final: 0.8209 (mmm)
REVERT: B  612 LYS cc_start: 0.9514 (tptp) cc_final: 0.9280 (tptm)
REVERT: B  621 ASP cc_start: 0.9725 (t0) cc_final: 0.9466 (t70)
REVERT: B  704 GLU cc_start: 0.9357 (pt0) cc_final: 0.9095 (pp20)
REVERT: B  813 MET cc_start: 0.9602 (tpt) cc_final: 0.8712 (tpp)
REVERT: B  828 ASP cc_start: 0.9312 (m-30) cc_final: 0.8219 (t0)
REVERT: B  838 VAL cc_start: 0.9438 (t) cc_final: 0.9091 (p)
REVERT: B  845 ILE cc_start: 0.9204 (mm) cc_final: 0.8980 (pt)
REVERT: B  846 MET cc_start: 0.9388 (mtm) cc_final: 0.8942 (mtp)
REVERT: B  957 MET cc_start: 0.8913 (mmp) cc_final: 0.8701 (mmm)
REVERT: B  962 GLU cc_start: 0.9300 (tt0) cc_final: 0.9095 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1303
  time to fit residues: 42.3132
Evaluate side-chains
  168 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 113 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 123 optimal weight:    5.9990
   chunk 151 optimal weight:    8.9990
   chunk 33 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9980
   chunk 208 optimal weight:    9.9990
   chunk 19 optimal weight:   30.0000
   chunk 141 optimal weight:   30.0000
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 381 HIS
** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 GLN
B 286 GLN
B 381 HIS
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 692 GLN
B 804 GLN
** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.066538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.041381 restraints weight = 180642.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.042824 restraints weight = 118136.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.043796 restraints weight = 85836.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.044559 restraints weight = 67962.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.044908 restraints weight = 56296.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.6023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  21107  Z= 0.196
  Angle     :  0.649  11.262  28863  Z= 0.344
  Chirality :  0.045   0.499   3215
  Planarity :  0.004   0.078   3397
  Dihedral  : 17.458 174.578   3463
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 16.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.18), residues: 2359
  helix:  0.88 (0.17), residues: 996
  sheet: -0.42 (0.27), residues: 397
  loop : -0.37 (0.21), residues: 966

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 831 
 TYR   0.022   0.002   TYR B 837 
 PHE   0.041   0.002   PHE B 596 
 TRP   0.033   0.002   TRP B 820 
 HIS   0.007   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (21107)
  covalent geometry    : angle       0.64861 (28863)
  hydrogen bonds       : bond        0.04781 (  931)
  hydrogen bonds       : angle       5.01910 ( 2595)

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

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

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.3519 (tmm) cc_final: 0.3269 (tmm)
REVERT: A  257 MET cc_start: 0.3286 (ptm) cc_final: 0.2854 (ptm)
REVERT: A  446 LEU cc_start: 0.9828 (mt) cc_final: 0.9613 (mt)
REVERT: A  467 MET cc_start: 0.9343 (mtp) cc_final: 0.8935 (ttt)
REVERT: A  483 ASN cc_start: 0.8950 (p0) cc_final: 0.8610 (m-40)
REVERT: A  493 MET cc_start: 0.9655 (tpp) cc_final: 0.9386 (tpp)
REVERT: A  586 MET cc_start: 0.9048 (mmp) cc_final: 0.8698 (tpp)
REVERT: A  698 TYR cc_start: 0.9480 (t80) cc_final: 0.8557 (t80)
REVERT: A  704 GLU cc_start: 0.9513 (tp30) cc_final: 0.9006 (tp30)
REVERT: A  756 MET cc_start: 0.9745 (mpp) cc_final: 0.9238 (tpp)
REVERT: A  775 LEU cc_start: 0.9518 (tp) cc_final: 0.9292 (tp)
REVERT: A  854 GLU cc_start: 0.9534 (mm-30) cc_final: 0.9155 (mm-30)
REVERT: A  957 MET cc_start: 0.9224 (mmp) cc_final: 0.8757 (mmm)
REVERT: A 1042 LEU cc_start: 0.9602 (mt) cc_final: 0.9394 (mt)
REVERT: B  447 ARG cc_start: 0.9252 (mtm-85) cc_final: 0.8901 (mtt-85)
REVERT: B  502 ASN cc_start: 0.9243 (t0) cc_final: 0.8999 (t0)
REVERT: B  573 LEU cc_start: 0.8897 (tt) cc_final: 0.8693 (pp)
REVERT: B  586 MET cc_start: 0.8485 (mmm) cc_final: 0.8159 (mmm)
REVERT: B  621 ASP cc_start: 0.9715 (t0) cc_final: 0.9456 (t70)
REVERT: B  704 GLU cc_start: 0.9320 (pt0) cc_final: 0.9063 (pp20)
REVERT: B  813 MET cc_start: 0.9523 (tpt) cc_final: 0.8712 (tpp)
REVERT: B  838 VAL cc_start: 0.9539 (t) cc_final: 0.9249 (p)
REVERT: B  841 LEU cc_start: 0.9808 (tp) cc_final: 0.9592 (tp)
REVERT: B  845 ILE cc_start: 0.9310 (mm) cc_final: 0.8974 (pt)
REVERT: B  846 MET cc_start: 0.9319 (mtm) cc_final: 0.9016 (mpp)
REVERT: B  858 TYR cc_start: 0.9007 (t80) cc_final: 0.8796 (t80)
REVERT: B  957 MET cc_start: 0.8906 (mmp) cc_final: 0.8687 (mmm)
REVERT: B  962 GLU cc_start: 0.9344 (tt0) cc_final: 0.9130 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.1143
  time to fit residues: 35.9948
Evaluate side-chains
  153 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 65 optimal weight:    9.9990
   chunk 219 optimal weight:    0.8980
   chunk 211 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 126 optimal weight:    8.9990
   chunk 63 optimal weight:    5.9990
   chunk 165 optimal weight:   10.0000
   chunk 161 optimal weight:    4.9990
   chunk 143 optimal weight:    9.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 308 ASN
A 381 HIS
** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 692 GLN
B 905 ASN
** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.063216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.038918 restraints weight = 186329.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.040238 restraints weight = 121826.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.041210 restraints weight = 89132.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.041552 restraints weight = 70015.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.042369 restraints weight = 59931.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.6862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  21107  Z= 0.252
  Angle     :  0.710   9.972  28863  Z= 0.381
  Chirality :  0.046   0.444   3215
  Planarity :  0.005   0.064   3397
  Dihedral  : 17.688 174.850   3463
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 21.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.18), residues: 2359
  helix:  0.57 (0.16), residues: 997
  sheet: -0.71 (0.27), residues: 387
  loop : -0.45 (0.21), residues: 975

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.031   0.001   ARG B 831 
 TYR   0.025   0.002   TYR B 837 
 PHE   0.031   0.002   PHE B 596 
 TRP   0.022   0.002   TRP A1170 
 HIS   0.008   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 (21107)
  covalent geometry    : angle       0.70993 (28863)
  hydrogen bonds       : bond        0.05110 (  931)
  hydrogen bonds       : angle       5.30979 ( 2595)

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

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

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 MET cc_start: 0.3202 (ptm) cc_final: 0.2787 (ptm)
REVERT: A  446 LEU cc_start: 0.9845 (mt) cc_final: 0.9574 (mt)
REVERT: A  467 MET cc_start: 0.9390 (mtp) cc_final: 0.8949 (ttt)
REVERT: A  475 MET cc_start: 0.9128 (mmp) cc_final: 0.8882 (mmp)
REVERT: A  483 ASN cc_start: 0.9019 (p0) cc_final: 0.8688 (m-40)
REVERT: A  493 MET cc_start: 0.9656 (tpp) cc_final: 0.9421 (tpp)
REVERT: A  586 MET cc_start: 0.9019 (mmp) cc_final: 0.8695 (tpp)
REVERT: A  617 LEU cc_start: 0.9398 (tp) cc_final: 0.9029 (tp)
REVERT: A  698 TYR cc_start: 0.9509 (t80) cc_final: 0.8593 (t80)
REVERT: A  704 GLU cc_start: 0.9468 (tp30) cc_final: 0.9022 (tp30)
REVERT: A  714 MET cc_start: 0.9635 (tpt) cc_final: 0.9214 (tpp)
REVERT: A  854 GLU cc_start: 0.9546 (mm-30) cc_final: 0.9321 (mm-30)
REVERT: A  858 TYR cc_start: 0.9083 (t80) cc_final: 0.8789 (t80)
REVERT: A  957 MET cc_start: 0.9194 (mmp) cc_final: 0.8730 (mmm)
REVERT: A 1042 LEU cc_start: 0.9569 (mt) cc_final: 0.9270 (mt)
REVERT: B   32 MET cc_start: 0.4417 (tpt) cc_final: 0.4130 (tpt)
REVERT: B  467 MET cc_start: 0.9340 (mtp) cc_final: 0.9098 (mtp)
REVERT: B  502 ASN cc_start: 0.9432 (t0) cc_final: 0.9201 (t0)
REVERT: B  586 MET cc_start: 0.8724 (mmm) cc_final: 0.8381 (mmm)
REVERT: B  621 ASP cc_start: 0.9676 (t0) cc_final: 0.9403 (t70)
REVERT: B  643 ASP cc_start: 0.9251 (m-30) cc_final: 0.8848 (p0)
REVERT: B  698 TYR cc_start: 0.9537 (t80) cc_final: 0.9113 (t80)
REVERT: B  704 GLU cc_start: 0.9301 (pt0) cc_final: 0.9079 (pp20)
REVERT: B  764 LYS cc_start: 0.9629 (mtpt) cc_final: 0.9378 (ttpt)
REVERT: B  813 MET cc_start: 0.9528 (tpt) cc_final: 0.8792 (tpp)
REVERT: B  838 VAL cc_start: 0.9535 (t) cc_final: 0.9266 (p)
REVERT: B  841 LEU cc_start: 0.9708 (tp) cc_final: 0.9502 (tp)
REVERT: B  845 ILE cc_start: 0.9357 (mm) cc_final: 0.9077 (mp)
REVERT: B  846 MET cc_start: 0.9286 (mtm) cc_final: 0.8965 (mpp)
REVERT: B  858 TYR cc_start: 0.9077 (t80) cc_final: 0.8504 (t80)
REVERT: B  957 MET cc_start: 0.8903 (mmp) cc_final: 0.8689 (mmm)
REVERT: B 1153 ASP cc_start: 0.9507 (t0) cc_final: 0.9205 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.1255
  time to fit residues: 36.2729
Evaluate side-chains
  136 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 174 optimal weight:    7.9990
   chunk 98 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 158 optimal weight:   20.0000
   chunk 49 optimal weight:    0.5980
   chunk 143 optimal weight:    0.9990
   chunk 20 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 3 optimal weight:    0.0040
   overall best weight:    1.1198

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

Flipped N/Q/H residues before XYZ refinement:
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 603 GLN
** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 880 ASN
** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 HIS
B 692 GLN
B 804 GLN
** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1099 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.066763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.041548 restraints weight = 179374.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.043013 restraints weight = 114859.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.044050 restraints weight = 81486.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.044617 restraints weight = 62982.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.045336 restraints weight = 51815.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.6746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  21107  Z= 0.127
  Angle     :  0.607   9.462  28863  Z= 0.320
  Chirality :  0.044   0.322   3215
  Planarity :  0.004   0.052   3397
  Dihedral  : 17.547 175.112   3463
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.18), residues: 2359
  helix:  0.86 (0.17), residues: 1008
  sheet: -0.64 (0.27), residues: 388
  loop : -0.38 (0.21), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 683 
 TYR   0.021   0.002   TYR A 637 
 PHE   0.017   0.002   PHE B 596 
 TRP   0.012   0.001   TRP A 157 
 HIS   0.007   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (21107)
  covalent geometry    : angle       0.60688 (28863)
  hydrogen bonds       : bond        0.04353 (  931)
  hydrogen bonds       : angle       4.98007 ( 2595)

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

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

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 MET cc_start: 0.3354 (ptm) cc_final: 0.2865 (ptm)
REVERT: A  467 MET cc_start: 0.9387 (mtp) cc_final: 0.8872 (ttt)
REVERT: A  483 ASN cc_start: 0.9039 (p0) cc_final: 0.8722 (m-40)
REVERT: A  493 MET cc_start: 0.9632 (tpp) cc_final: 0.9407 (tpp)
REVERT: A  586 MET cc_start: 0.9093 (mmp) cc_final: 0.8745 (tpp)
REVERT: A  617 LEU cc_start: 0.9378 (tp) cc_final: 0.9071 (tp)
REVERT: A  698 TYR cc_start: 0.9445 (t80) cc_final: 0.8470 (t80)
REVERT: A  704 GLU cc_start: 0.9484 (tp30) cc_final: 0.8978 (tp30)
REVERT: A  714 MET cc_start: 0.9621 (tpt) cc_final: 0.9218 (tpp)
REVERT: A  756 MET cc_start: 0.9706 (mpp) cc_final: 0.9198 (tpp)
REVERT: A  846 MET cc_start: 0.9651 (mtm) cc_final: 0.9348 (ptp)
REVERT: A  854 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9199 (mm-30)
REVERT: A  957 MET cc_start: 0.9176 (mmp) cc_final: 0.8664 (mmm)
REVERT: A 1042 LEU cc_start: 0.9562 (mt) cc_final: 0.9274 (mt)
REVERT: B   32 MET cc_start: 0.3664 (tpt) cc_final: 0.3402 (tpt)
REVERT: B   42 MET cc_start: 0.8956 (pmm) cc_final: 0.8743 (pmm)
REVERT: B  257 MET cc_start: 0.1050 (ttt) cc_final: 0.0765 (ttt)
REVERT: B  467 MET cc_start: 0.9305 (mtp) cc_final: 0.8439 (mpp)
REVERT: B  586 MET cc_start: 0.8690 (mmm) cc_final: 0.8051 (mmm)
REVERT: B  621 ASP cc_start: 0.9709 (t0) cc_final: 0.9466 (t70)
REVERT: B  643 ASP cc_start: 0.9264 (m-30) cc_final: 0.8890 (p0)
REVERT: B  698 TYR cc_start: 0.9567 (t80) cc_final: 0.9044 (t80)
REVERT: B  704 GLU cc_start: 0.9348 (pt0) cc_final: 0.9012 (pp20)
REVERT: B  755 ASP cc_start: 0.9652 (p0) cc_final: 0.9450 (p0)
REVERT: B  764 LYS cc_start: 0.9542 (mtpt) cc_final: 0.9301 (ttpt)
REVERT: B  813 MET cc_start: 0.9565 (tpt) cc_final: 0.8824 (tpp)
REVERT: B  838 VAL cc_start: 0.9563 (t) cc_final: 0.9259 (p)
REVERT: B  841 LEU cc_start: 0.9782 (tp) cc_final: 0.9552 (tp)
REVERT: B  845 ILE cc_start: 0.9293 (mm) cc_final: 0.9063 (mm)
REVERT: B  846 MET cc_start: 0.9328 (mtm) cc_final: 0.8831 (mpp)
REVERT: B  858 TYR cc_start: 0.8974 (t80) cc_final: 0.8555 (t80)
REVERT: B  865 LEU cc_start: 0.9549 (mm) cc_final: 0.9287 (pp)
REVERT: B 1153 ASP cc_start: 0.9507 (t0) cc_final: 0.9202 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.1269
  time to fit residues: 40.4403
Evaluate side-chains
  156 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 147 optimal weight:   20.0000
   chunk 144 optimal weight:   40.0000
   chunk 170 optimal weight:    0.3980
   chunk 84 optimal weight:   10.0000
   chunk 115 optimal weight:    0.1980
   chunk 225 optimal weight:    9.9990
   chunk 95 optimal weight:    6.9990
   chunk 0 optimal weight:   50.0000
   chunk 176 optimal weight:    9.9990
   chunk 174 optimal weight:    5.9990
   overall best weight:    3.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 692 GLN
B 905 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.064731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.040052 restraints weight = 184055.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.041430 restraints weight = 119065.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.042428 restraints weight = 86094.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.043138 restraints weight = 67046.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.043399 restraints weight = 55258.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.7032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  21107  Z= 0.178
  Angle     :  0.631  10.378  28863  Z= 0.338
  Chirality :  0.044   0.309   3215
  Planarity :  0.004   0.051   3397
  Dihedral  : 17.530 175.780   3463
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 16.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.18), residues: 2359
  helix:  0.82 (0.16), residues: 1015
  sheet: -0.71 (0.27), residues: 404
  loop : -0.41 (0.22), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 831 
 TYR   0.017   0.002   TYR B1067 
 PHE   0.017   0.002   PHE B 785 
 TRP   0.027   0.002   TRP A1170 
 HIS   0.007   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (21107)
  covalent geometry    : angle       0.63143 (28863)
  hydrogen bonds       : bond        0.04561 (  931)
  hydrogen bonds       : angle       5.10936 ( 2595)

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

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

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4718 Ramachandran restraints generated.
    2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 MET cc_start: 0.3321 (ptm) cc_final: 0.2747 (ptm)
REVERT: A  446 LEU cc_start: 0.9851 (mt) cc_final: 0.9628 (mt)
REVERT: A  467 MET cc_start: 0.9377 (mtp) cc_final: 0.8870 (ttt)
REVERT: A  475 MET cc_start: 0.9051 (mmp) cc_final: 0.8787 (mmp)
REVERT: A  483 ASN cc_start: 0.9042 (p0) cc_final: 0.8727 (t0)
REVERT: A  493 MET cc_start: 0.9667 (tpp) cc_final: 0.9459 (tpp)
REVERT: A  531 TYR cc_start: 0.9041 (p90) cc_final: 0.8680 (p90)
REVERT: A  586 MET cc_start: 0.9088 (mmp) cc_final: 0.8730 (tpp)
REVERT: A  617 LEU cc_start: 0.9406 (tp) cc_final: 0.9066 (tp)
REVERT: A  698 TYR cc_start: 0.9450 (t80) cc_final: 0.8546 (t80)
REVERT: A  701 ASP cc_start: 0.9725 (t70) cc_final: 0.9474 (t0)
REVERT: A  704 GLU cc_start: 0.9445 (tp30) cc_final: 0.8976 (tp30)
REVERT: A  714 MET cc_start: 0.9634 (tpt) cc_final: 0.9182 (tpp)
REVERT: A  756 MET cc_start: 0.9716 (mpp) cc_final: 0.9234 (tpp)
REVERT: A  846 MET cc_start: 0.9690 (mtm) cc_final: 0.9433 (ptp)
REVERT: A  854 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9244 (mm-30)
REVERT: A  858 TYR cc_start: 0.9037 (t80) cc_final: 0.8792 (t80)
REVERT: A  957 MET cc_start: 0.9175 (mmp) cc_final: 0.8714 (mmm)
REVERT: A 1042 LEU cc_start: 0.9604 (mt) cc_final: 0.9364 (mt)
REVERT: B   32 MET cc_start: 0.4381 (tpt) cc_final: 0.4077 (tpt)
REVERT: B   42 MET cc_start: 0.8988 (pmm) cc_final: 0.8764 (pmm)
REVERT: B  257 MET cc_start: 0.0395 (ttt) cc_final: 0.0127 (ttt)
REVERT: B  447 ARG cc_start: 0.9247 (mtm-85) cc_final: 0.8866 (mtt-85)
REVERT: B  576 LEU cc_start: 0.8671 (tp) cc_final: 0.8314 (tp)
REVERT: B  586 MET cc_start: 0.8757 (mmm) cc_final: 0.8430 (mmm)
REVERT: B  621 ASP cc_start: 0.9691 (t0) cc_final: 0.9434 (t70)
REVERT: B  643 ASP cc_start: 0.9230 (m-30) cc_final: 0.8882 (p0)
REVERT: B  698 TYR cc_start: 0.9424 (t80) cc_final: 0.9038 (t80)
REVERT: B  704 GLU cc_start: 0.9313 (pt0) cc_final: 0.9064 (pp20)
REVERT: B  764 LYS cc_start: 0.9571 (mtpt) cc_final: 0.9336 (ttpt)
REVERT: B  813 MET cc_start: 0.9527 (tpt) cc_final: 0.8755 (tpp)
REVERT: B  838 VAL cc_start: 0.9539 (t) cc_final: 0.9238 (p)
REVERT: B  841 LEU cc_start: 0.9754 (tp) cc_final: 0.9523 (tp)
REVERT: B  845 ILE cc_start: 0.9291 (mm) cc_final: 0.9011 (mp)
REVERT: B  846 MET cc_start: 0.9290 (mtm) cc_final: 0.8831 (mpp)
REVERT: B  858 TYR cc_start: 0.9012 (t80) cc_final: 0.8528 (t80)
REVERT: B  865 LEU cc_start: 0.9607 (mm) cc_final: 0.9327 (pp)
REVERT: B 1153 ASP cc_start: 0.9529 (t0) cc_final: 0.9246 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.1223
  time to fit residues: 36.4153
Evaluate side-chains
  145 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 105 optimal weight:    7.9990
   chunk 154 optimal weight:   20.0000
   chunk 75 optimal weight:    2.9990
   chunk 235 optimal weight:    2.9990
   chunk 47 optimal weight:   20.0000
   chunk 169 optimal weight:    7.9990
   chunk 2 optimal weight:    9.9990
   chunk 73 optimal weight:    3.9990
   chunk 6 optimal weight:   30.0000
   chunk 201 optimal weight:    0.9980
   chunk 239 optimal weight:    8.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 308 ASN
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 ASN
B 409 ASN
B 692 GLN
** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.063844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.039427 restraints weight = 183862.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.040780 restraints weight = 118848.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.041742 restraints weight = 85680.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.042299 restraints weight = 67067.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.043003 restraints weight = 55312.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.7333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  21107  Z= 0.188
  Angle     :  0.638  11.676  28863  Z= 0.342
  Chirality :  0.044   0.276   3215
  Planarity :  0.004   0.050   3397
  Dihedral  : 17.617 177.111   3463
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 17.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.18), residues: 2359
  helix:  0.75 (0.16), residues: 1015
  sheet: -0.75 (0.27), residues: 399
  loop : -0.37 (0.22), residues: 945

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 684 
 TYR   0.023   0.002   TYR B 591 
 PHE   0.045   0.002   PHE B 596 
 TRP   0.038   0.002   TRP B1170 
 HIS   0.006   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (21107)
  covalent geometry    : angle       0.63845 (28863)
  hydrogen bonds       : bond        0.04611 (  931)
  hydrogen bonds       : angle       5.14199 ( 2595)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3884.96 seconds
wall clock time: 68 minutes 4.07 seconds (4084.07 seconds total)