Starting phenix.real_space_refine
on Sat Jun 14 00:50:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u7r_41990/06_2025/8u7r_41990.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u7r_41990/06_2025/8u7r_41990.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u7r_41990/06_2025/8u7r_41990.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u7r_41990/06_2025/8u7r_41990.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u7r_41990/06_2025/8u7r_41990.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u7r_41990/06_2025/8u7r_41990.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.010 sd=   0.074
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      76      5.16       5
     C   10156      2.51       5
     N    2549      2.21       5
     O    2817      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 15601
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 985, 7601
          Classifications: {'peptide': 985}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 955}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 184
          Unresolved non-hydrogen angles: 239
          Unresolved non-hydrogen dihedrals: 149
          Unresolved non-hydrogen chiralities: 27
          Planarities with less than four sites: {'PHE:plan': 5, 'GLU:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 84
    Chain: "B"
      Number of atoms: 7615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 986, 7615
          Classifications: {'peptide': 986}
          Incomplete info: {'truncation_to_alanine': 47}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 956}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 179
          Unresolved non-hydrogen angles: 232
          Unresolved non-hydrogen dihedrals: 144
          Unresolved non-hydrogen chiralities: 26
          Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 82
    Chain: "A"
      Number of atoms: 213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 213
          Unusual residues: {'AJP': 2, 'POV': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 111
          Unresolved non-hydrogen chiralities: 18
    Chain: "B"
      Number of atoms: 172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 172
          Unusual residues: {'AJP': 2, 'POV': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 79
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 18
  Time building chain proxies: 9.70, per 1000 atoms: 0.62
  Number of scatterers: 15601
  At special positions: 0
  Unit cell: (108.9, 136.4, 128.7, 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      76     16.00
     P       3     15.00
     O    2817      8.00
     N    2549      7.00
     C   10156      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: 4.07
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3714

  Finding SS restraints...
    Secondary structure from input PDB file:
      81 helices and 8 sheets defined
      75.5% alpha, 4.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 77 through 94
    Processing helix  chain 'A' and resid 102 through 120
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.501A  pdb=" N   GLU A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   ASP A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   VAL A 130 " --> pdb=" O   HIS A 126 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   HIS A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 153
      removed outlier: 3.781A  pdb=" N   LEU A 138 " --> pdb=" O   ASP A 134 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   LEU A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 155 through 162
      removed outlier: 4.007A  pdb=" N   SER A 162 " --> pdb=" O   THR A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 188
      removed outlier: 3.580A  pdb=" N   ASN A 187 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 205
      removed outlier: 3.803A  pdb=" N   MET A 205 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 220
      removed outlier: 3.888A  pdb=" N   VAL A 213 " --> pdb=" O   ASP A 209 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 254
      removed outlier: 3.809A  pdb=" N   VAL A 243 " --> pdb=" O   GLY A 239 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE A 254 " --> pdb=" O   LYS A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 291
      removed outlier: 5.087A  pdb=" N   GLY A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      Proline residue:  A 276  - end of helix
    Processing helix  chain 'A' and resid 298 through 319
      removed outlier: 3.655A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 337
      removed outlier: 4.293A  pdb=" N   LEU A 325 " --> pdb=" O   VAL A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 375
    Processing helix  chain 'A' and resid 376 through 379
      removed outlier: 3.740A  pdb=" N   ALA A 379 " --> pdb=" O   ALA A 376 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 376 through 379'
    Processing helix  chain 'A' and resid 381 through 414
      removed outlier: 4.322A  pdb=" N   LEU A 388 " --> pdb=" O   ASP A 384 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   ILE A 389 " --> pdb=" O   TRP A 385 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ILE A 390 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ILE A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
      Proline residue:  A 408  - end of helix
    Processing helix  chain 'A' and resid 418 through 427
      removed outlier: 3.681A  pdb=" N   TRP A 427 " --> pdb=" O   VAL A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 447
      removed outlier: 4.100A  pdb=" N   LEU A 436 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY A 447 " --> pdb=" O   GLU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 481
      removed outlier: 4.328A  pdb=" N   VAL A 468 " --> pdb=" O   VAL A 464 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   ALA A 471 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 485
      removed outlier: 3.644A  pdb=" N   ASP A 485 " --> pdb=" O   GLY A 482 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 482 through 485'
    Processing helix  chain 'A' and resid 487 through 513
    Processing helix  chain 'A' and resid 522 through 529
    Processing helix  chain 'A' and resid 571 through 600
    Processing helix  chain 'A' and resid 604 through 621
    Processing helix  chain 'A' and resid 628 through 636
    Processing helix  chain 'A' and resid 637 through 640
      removed outlier: 3.894A  pdb=" N   ILE A 640 " --> pdb=" O   ILE A 637 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 637 through 640'
    Processing helix  chain 'A' and resid 641 through 653
      removed outlier: 3.633A  pdb=" N   LEU A 651 " --> pdb=" O   LYS A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 700
      removed outlier: 3.719A  pdb=" N   VAL A 693 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      Proline residue:  A 694  - end of helix
    Processing helix  chain 'A' and resid 728 through 757
      removed outlier: 3.690A  pdb=" N   ALA A 747 " --> pdb=" O   TYR A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 774
      removed outlier: 3.872A  pdb=" N   PHE A 766 " --> pdb=" O   HIS A 762 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   PHE A 769 " --> pdb=" O   LYS A 765 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA A 774 " --> pdb=" O   ILE A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 854
      Proline residue:  A 819  - end of helix
      removed outlier: 3.986A  pdb=" N   GLN A 832 " --> pdb=" O   LYS A 828 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 857
      No H-bonds generated for 'chain 'A' and resid 855 through 857'
    Processing helix  chain 'A' and resid 860 through 889
      removed outlier: 4.061A  pdb=" N   HIS A 889 " --> pdb=" O   LEU A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 919
      removed outlier: 4.162A  pdb=" N   ALA A 893 " --> pdb=" O   HIS A 889 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 923 through 943
      removed outlier: 3.547A  pdb=" N   ALA A 927 " --> pdb=" O   ASP A 923 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ASN A 943 " --> pdb=" O   LYS A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 958
    Processing helix  chain 'A' and resid 966 through 977
      removed outlier: 3.693A  pdb=" N   ARG A 976 " --> pdb=" O   PHE A 972 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1043 through 1049
    Processing helix  chain 'A' and resid 1069 through 1080
      removed outlier: 3.591A  pdb=" N   PHE A1080 " --> pdb=" O   ALA A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1107
      Proline residue:  A1101  - end of helix
    Processing helix  chain 'A' and resid 1113 through 1124
      removed outlier: 3.950A  pdb=" N   GLY A1124 " --> pdb=" O   HIS A1120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 94
    Processing helix  chain 'B' and resid 102 through 120
    Processing helix  chain 'B' and resid 120 through 132
      removed outlier: 3.508A  pdb=" N   GLU B 124 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   ASP B 129 " --> pdb=" O   GLU B 125 " (cutoff:3.500A)
      removed outlier: 5.458A  pdb=" N   VAL B 130 " --> pdb=" O   HIS B 126 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   HIS B 132 " --> pdb=" O   ARG B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 153
      removed outlier: 3.810A  pdb=" N   LEU B 138 " --> pdb=" O   ASP B 134 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   LEU B 143 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      Proline residue:  B 144  - end of helix
    Processing helix  chain 'B' and resid 155 through 162
      removed outlier: 3.986A  pdb=" N   SER B 162 " --> pdb=" O   THR B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 188
      removed outlier: 3.592A  pdb=" N   ASN B 187 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 204
    Processing helix  chain 'B' and resid 209 through 220
      removed outlier: 4.210A  pdb=" N   VAL B 213 " --> pdb=" O   ASP B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 254
      removed outlier: 3.562A  pdb=" N   CYS B 240 " --> pdb=" O   LEU B 236 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   PHE B 254 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 291
      removed outlier: 4.721A  pdb=" N   GLY B 275 " --> pdb=" O   VAL B 271 " (cutoff:3.500A)
      Proline residue:  B 276  - end of helix
    Processing helix  chain 'B' and resid 298 through 318
      removed outlier: 3.667A  pdb=" N   THR B 302 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 337
      removed outlier: 3.763A  pdb=" N   GLY B 323 " --> pdb=" O   LEU B 319 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   VAL B 324 " --> pdb=" O   GLU B 320 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   LEU B 325 " --> pdb=" O   VAL B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 375
    Processing helix  chain 'B' and resid 376 through 379
      removed outlier: 3.713A  pdb=" N   ALA B 379 " --> pdb=" O   ALA B 376 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 376 through 379'
    Processing helix  chain 'B' and resid 381 through 414
      removed outlier: 4.318A  pdb=" N   LEU B 388 " --> pdb=" O   ASP B 384 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   ILE B 389 " --> pdb=" O   TRP B 385 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ILE B 390 " --> pdb=" O   PHE B 386 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE B 403 " --> pdb=" O   ARG B 399 " (cutoff:3.500A)
      Proline residue:  B 408  - end of helix
    Processing helix  chain 'B' and resid 418 through 427
      removed outlier: 3.690A  pdb=" N   TRP B 427 " --> pdb=" O   VAL B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 447
      removed outlier: 3.714A  pdb=" N   GLY B 447 " --> pdb=" O   GLU B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 481
      removed outlier: 4.324A  pdb=" N   VAL B 468 " --> pdb=" O   VAL B 464 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   ALA B 471 " --> pdb=" O   LEU B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 485
      removed outlier: 3.668A  pdb=" N   ASP B 485 " --> pdb=" O   GLY B 482 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 482 through 485'
    Processing helix  chain 'B' and resid 487 through 513
    Processing helix  chain 'B' and resid 522 through 529
    Processing helix  chain 'B' and resid 571 through 600
      removed outlier: 3.510A  pdb=" N   PHE B 598 " --> pdb=" O   TYR B 594 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   HIS B 600 " --> pdb=" O   LYS B 596 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 604 through 621
    Processing helix  chain 'B' and resid 628 through 636
    Processing helix  chain 'B' and resid 637 through 639
      No H-bonds generated for 'chain 'B' and resid 637 through 639'
    Processing helix  chain 'B' and resid 640 through 653
      removed outlier: 3.997A  pdb=" N   LEU B 644 " --> pdb=" O   ILE B 640 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU B 651 " --> pdb=" O   LYS B 647 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 678 through 700
      removed outlier: 3.510A  pdb=" N   VAL B 682 " --> pdb=" O   MET B 678 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   VAL B 693 " --> pdb=" O   VAL B 689 " (cutoff:3.500A)
      Proline residue:  B 694  - end of helix
    Processing helix  chain 'B' and resid 728 through 757
    Processing helix  chain 'B' and resid 761 through 774
    Processing helix  chain 'B' and resid 808 through 812
      removed outlier: 3.790A  pdb=" N   LEU B 811 " --> pdb=" O   LEU B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 813 through 854
      Proline residue:  B 819  - end of helix
      removed outlier: 3.534A  pdb=" N   GLY B 827 " --> pdb=" O   LEU B 823 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   GLN B 832 " --> pdb=" O   LYS B 828 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 855 through 857
      No H-bonds generated for 'chain 'B' and resid 855 through 857'
    Processing helix  chain 'B' and resid 860 through 889
      removed outlier: 4.055A  pdb=" N   HIS B 889 " --> pdb=" O   LEU B 885 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 889 through 919
      removed outlier: 4.173A  pdb=" N   ALA B 893 " --> pdb=" O   HIS B 889 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 923 through 943
      removed outlier: 3.556A  pdb=" N   ALA B 927 " --> pdb=" O   ASP B 923 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ASN B 943 " --> pdb=" O   LYS B 939 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 952 through 958
    Processing helix  chain 'B' and resid 966 through 977
      removed outlier: 3.679A  pdb=" N   ARG B 976 " --> pdb=" O   PHE B 972 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1043 through 1049
    Processing helix  chain 'B' and resid 1069 through 1080
      removed outlier: 3.602A  pdb=" N   PHE B1080 " --> pdb=" O   ALA B1076 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1085 through 1107
      Proline residue:  B1101  - end of helix
    Processing helix  chain 'B' and resid 1113 through 1124
      removed outlier: 3.870A  pdb=" N   GLY B1124 " --> pdb=" O   HIS B1120 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982
      removed outlier: 6.146A  pdb=" N   GLN A1064 " --> pdb=" O   VAL A1002 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1032 through 1036
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1127
      removed outlier: 3.514A  pdb=" N   TYR A1125 " --> pdb=" O   VAL A1188 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   VAL A1188 " --> pdb=" O   TYR A1125 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   VAL A1127 " --> pdb=" O   LEU A1186 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   LEU A1186 " --> pdb=" O   VAL A1127 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   PHE A1187 " --> pdb=" O   VAL A1145 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   VAL A1145 " --> pdb=" O   PHE A1187 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   VAL A1189 " --> pdb=" O   GLU A1143 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137
    Processing sheet with id=AA5, first strand: chain 'B' and resid 978 through 982
      removed outlier: 5.936A  pdb=" N   GLN B1064 " --> pdb=" O   VAL B1002 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1032 through 1036
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1125 through 1127
      removed outlier: 3.532A  pdb=" N   TYR B1125 " --> pdb=" O   VAL B1188 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   VAL B1188 " --> pdb=" O   TYR B1125 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   VAL B1127 " --> pdb=" O   LEU B1186 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   LEU B1186 " --> pdb=" O   VAL B1127 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   PHE B1187 " --> pdb=" O   VAL B1145 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   VAL B1145 " --> pdb=" O   PHE B1187 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   VAL B1189 " --> pdb=" O   GLU B1143 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   VAL B1145 " --> pdb=" O   ILE B1167 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1135 through 1137

    1106 hydrogen bonds defined for protein.
    3273 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.74

  Time building geometry restraints manager: 4.73 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2713
        1.33 -     1.45: 3830
        1.45 -     1.57: 9231
        1.57 -     1.69: 6
        1.69 -     1.81: 140
  Bond restraints: 15920
  Sorted by residual:
  bond pdb=" CA  LYS B  76 "
       pdb=" C   LYS B  76 "
    ideal  model  delta    sigma   weight residual
    1.522  1.481  0.042 1.20e-02 6.94e+03 1.20e+01
  bond pdb=" CA  LYS A  76 "
       pdb=" C   LYS A  76 "
    ideal  model  delta    sigma   weight residual
    1.522  1.482  0.041 1.20e-02 6.94e+03 1.14e+01
  bond pdb=" C   LYS A  76 "
       pdb=" O   LYS A  76 "
    ideal  model  delta    sigma   weight residual
    1.236  1.206  0.029 1.21e-02 6.83e+03 5.93e+00
  bond pdb=" C   LYS B  76 "
       pdb=" O   LYS B  76 "
    ideal  model  delta    sigma   weight residual
    1.236  1.207  0.029 1.21e-02 6.83e+03 5.59e+00
  bond pdb=" CA  LYS B  76 "
       pdb=" CB  LYS B  76 "
    ideal  model  delta    sigma   weight residual
    1.531  1.495  0.036 1.52e-02 4.33e+03 5.49e+00
  ... (remaining 15915 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 21343
        2.39 -     4.78: 256
        4.78 -     7.16: 46
        7.16 -     9.55: 10
        9.55 -    11.94: 2
  Bond angle restraints: 21657
  Sorted by residual:
  angle pdb=" CA  VAL B 693 "
        pdb=" C   VAL B 693 "
        pdb=" N   PRO B 694 "
      ideal   model   delta    sigma   weight residual
     120.83  117.55    3.28 6.10e-01 2.69e+00 2.89e+01
  angle pdb=" CA  VAL A 693 "
        pdb=" C   VAL A 693 "
        pdb=" N   PRO A 694 "
      ideal   model   delta    sigma   weight residual
     120.83  117.60    3.23 6.10e-01 2.69e+00 2.80e+01
  angle pdb=" N   ASN B 685 "
        pdb=" CA  ASN B 685 "
        pdb=" C   ASN B 685 "
      ideal   model   delta    sigma   weight residual
     111.11  106.40    4.71 1.20e+00 6.94e-01 1.54e+01
  angle pdb=" CA  LEU A 216 "
        pdb=" CB  LEU A 216 "
        pdb=" CG  LEU A 216 "
      ideal   model   delta    sigma   weight residual
     116.30  128.24  -11.94 3.50e+00 8.16e-02 1.16e+01
  angle pdb=" C   VAL A 693 "
        pdb=" CA  VAL A 693 "
        pdb=" CB  VAL A 693 "
      ideal   model   delta    sigma   weight residual
     114.00  109.54    4.46 1.31e+00 5.83e-01 1.16e+01
  ... (remaining 21652 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.29: 9032
       23.29 -    46.58: 823
       46.58 -    69.87: 142
       69.87 -    93.16: 14
       93.16 -   116.45: 28
  Dihedral angle restraints: 10039
    sinusoidal: 4316
      harmonic: 5723
  Sorted by residual:
  dihedral pdb=" C02 AJP B1402 "
           pdb=" C85 AJP B1402 "
           pdb=" O84 AJP B1402 "
           pdb=" C05 AJP B1402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.60   58.85 -116.45     1      3.00e+01 1.11e-03 1.54e+01
  dihedral pdb=" C02 AJP A1404 "
           pdb=" C85 AJP A1404 "
           pdb=" O84 AJP A1404 "
           pdb=" C05 AJP A1404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.60   58.23 -115.83     1      3.00e+01 1.11e-03 1.53e+01
  dihedral pdb=" C02 AJP B1403 "
           pdb=" C85 AJP B1403 "
           pdb=" O84 AJP B1403 "
           pdb=" C05 AJP B1403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.60   57.17 -114.77     1      3.00e+01 1.11e-03 1.51e+01
  ... (remaining 10036 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1986
       0.042 -    0.084: 494
       0.084 -    0.126: 139
       0.126 -    0.168: 24
       0.168 -    0.211: 8
  Chirality restraints: 2651
  Sorted by residual:
  chirality pdb=" C10 AJP B1403 "
            pdb=" C08 AJP B1403 "
            pdb=" C11 AJP B1403 "
            pdb=" O82 AJP B1403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.61    2.40    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" C10 AJP A1403 "
            pdb=" C08 AJP A1403 "
            pdb=" C11 AJP A1403 "
            pdb=" O82 AJP A1403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.61    2.40    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" C10 AJP A1404 "
            pdb=" C08 AJP A1404 "
            pdb=" C11 AJP A1404 "
            pdb=" O82 AJP A1404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.61    2.41    0.20 2.00e-01 2.50e+01 9.74e-01
  ... (remaining 2648 not shown)

  Planarity restraints: 2627
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 641 "    0.048 5.00e-02 4.00e+02   7.23e-02 8.36e+00
        pdb=" N   PRO B 642 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO B 642 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 642 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 641 "    0.044 5.00e-02 4.00e+02   6.57e-02 6.92e+00
        pdb=" N   PRO A 642 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A 642 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 642 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 209 "    0.029 5.00e-02 4.00e+02   4.32e-02 2.99e+00
        pdb=" N   PRO A 210 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A 210 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 210 "    0.024 5.00e-02 4.00e+02
  ... (remaining 2624 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2777
        2.77 -     3.30: 15054
        3.30 -     3.83: 25284
        3.83 -     4.37: 25193
        4.37 -     4.90: 46557
  Nonbonded interactions: 114865
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 478 "
            pdb=" OG  SER A 484 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   LEU B 478 "
            pdb=" OG  SER B 484 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   GLN B 140 "
            pdb=" OH  TYR B 312 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" NH2 ARG A 646 "
            pdb=" OD1 ASN A 826 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" NH2 ARG B 646 "
            pdb=" OD1 ASN B 826 "
     model   vdw
     2.323 3.120
  ... (remaining 114860 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 75 through 728 or (resid 729 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 730 through 1192 or (resid 1401 and (name C \ 
1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ 
 C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or n \ 
ame C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39  \ 
or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name  \ 
O31 or name O32 or name P or name C210 or name C211 or name C212 or name C213 or \ 
 name C214 or name C215 or name C216 or name C310 or name C311 or name C312 or n \ 
ame C313 or name C314)) or resid 1403))
  selection = (chain 'B' and (resid 75 through 676 or resid 678 through 698 or (resid 699 thro \ 
ugh 700 and (name N or name CA or name C or name O or name CB )) or resid 727 th \ 
rough 1192 or resid 1401 or resid 1403))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.160
  Process input model:                     36.560
  Find NCS groups from input model:        0.740
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
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      :  0.003   0.043  15920  Z= 0.191
  Angle     :  0.677  11.941  21657  Z= 0.352
  Chirality :  0.042   0.211   2651
  Planarity :  0.004   0.072   2627
  Dihedral  : 18.386 116.447   6325
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 25.84 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.19), residues: 1947
  helix:  1.73 (0.14), residues: 1391
  sheet:  0.44 (0.48), residues: 112
  loop : -1.32 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 635 
 HIS   0.006   0.001   HIS B1120 
 PHE   0.018   0.001   PHE B 248 
 TYR   0.014   0.001   TYR B 309 
 ARG   0.003   0.000   ARG A 585 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11349 ( 1106)
  hydrogen bonds       : angle       4.37670 ( 3273)
  covalent geometry    : bond        0.00343 (15920)
  covalent geometry    : angle       0.67706 (21657)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 1.717 
Fit side-chains
REVERT: A  199 MET cc_start: 0.8361 (mmm) cc_final: 0.7583 (mpp)
REVERT: B  295 ASN cc_start: 0.7223 (t0) cc_final: 0.6989 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.2609
  time to fit residues: 61.1309
Evaluate side-chains
  128 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 165 optimal weight:    8.9990
   chunk 148 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 100 optimal weight:    9.9990
   chunk 79 optimal weight:    0.0070
   chunk 153 optimal weight:    9.9990
   chunk 59 optimal weight:    7.9990
   chunk 93 optimal weight:    8.9990
   chunk 114 optimal weight:    5.9990
   chunk 177 optimal weight:    0.9980
   overall best weight:    1.7802

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

Flipped N/Q/H residues before XYZ refinement:
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1120 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.148277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.114899 restraints weight = 25033.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.113686 restraints weight = 27528.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.115320 restraints weight = 24568.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.0776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15920  Z= 0.158
  Angle     :  0.585  11.442  21657  Z= 0.292
  Chirality :  0.038   0.149   2651
  Planarity :  0.004   0.070   2627
  Dihedral  :  9.703  80.031   2887
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 26.03 %
    Favored  : 71.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.19), residues: 1947
  helix:  2.13 (0.14), residues: 1398
  sheet:  1.29 (0.49), residues: 94
  loop : -1.29 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 419 
 HIS   0.006   0.001   HIS A1120 
 PHE   0.011   0.001   PHE B 195 
 TYR   0.023   0.001   TYR B 309 
 ARG   0.005   0.000   ARG B 646 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05646 ( 1106)
  hydrogen bonds       : angle       3.75582 ( 3273)
  covalent geometry    : bond        0.00362 (15920)
  covalent geometry    : angle       0.58476 (21657)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 138
  time to evaluate  : 1.861 
Fit side-chains
REVERT: A  199 MET cc_start: 0.8623 (mmm) cc_final: 0.7933 (tpp)
REVERT: B  199 MET cc_start: 0.8449 (mmm) cc_final: 0.7762 (mpp)
REVERT: B  295 ASN cc_start: 0.7548 (t0) cc_final: 0.7308 (t0)
  outliers start: 46
  outliers final: 17
  residues processed: 179
  average time/residue: 0.2343
  time to fit residues: 66.2685
Evaluate side-chains
  143 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 1.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  878 VAL
Chi-restraints excluded: chain A residue 1073 MET
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  837 TYR
Chi-restraints excluded: chain B residue  878 VAL
Chi-restraints excluded: chain B residue 1081 THR
Chi-restraints excluded: chain B residue 1167 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 185 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 157 optimal weight:    9.9990
   chunk 68 optimal weight:    9.9990
   chunk 67 optimal weight:    4.9990
   chunk 113 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 137 optimal weight:    3.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A1120 HIS
** B1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.149160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.114720 restraints weight = 25051.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.114324 restraints weight = 23551.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.115776 restraints weight = 23432.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.0905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15920  Z= 0.131
  Angle     :  0.522   8.227  21657  Z= 0.265
  Chirality :  0.037   0.138   2651
  Planarity :  0.004   0.076   2627
  Dihedral  :  8.046  81.332   2887
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 26.03 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.21 (0.19), residues: 1947
  helix:  2.31 (0.14), residues: 1399
  sheet:  1.06 (0.49), residues: 98
  loop : -1.27 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 419 
 HIS   0.007   0.001   HIS A1120 
 PHE   0.009   0.001   PHE A 248 
 TYR   0.021   0.001   TYR B 309 
 ARG   0.002   0.000   ARG B 646 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05112 ( 1106)
  hydrogen bonds       : angle       3.57041 ( 3273)
  covalent geometry    : bond        0.00288 (15920)
  covalent geometry    : angle       0.52161 (21657)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 139
  time to evaluate  : 1.919 
Fit side-chains
REVERT: A  199 MET cc_start: 0.8623 (mmm) cc_final: 0.8110 (tpp)
REVERT: B  199 MET cc_start: 0.8464 (mmm) cc_final: 0.8092 (tpp)
REVERT: B  295 ASN cc_start: 0.7531 (t0) cc_final: 0.7287 (t0)
REVERT: B  512 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9031 (tp)
REVERT: B  853 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7069 (tp)
  outliers start: 64
  outliers final: 30
  residues processed: 194
  average time/residue: 0.2931
  time to fit residues: 93.4253
Evaluate side-chains
  160 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 3.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  172 PHE
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  878 VAL
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1073 MET
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1167 ILE
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  172 PHE
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  837 TYR
Chi-restraints excluded: chain B residue  853 ILE
Chi-restraints excluded: chain B residue  878 VAL
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  941 LEU
Chi-restraints excluded: chain B residue  973 ILE
Chi-restraints excluded: chain B residue  989 VAL
Chi-restraints excluded: chain B residue 1081 THR
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1167 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 177 optimal weight:    8.9990
   chunk 78 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 109 optimal weight:    0.0010
   chunk 176 optimal weight:    0.9980
   chunk 83 optimal weight:    6.9990
   chunk 127 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 162 optimal weight:    5.9990
   overall best weight:    0.6986

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

Flipped N/Q/H residues before XYZ refinement:
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1120 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.150848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.116654 restraints weight = 25142.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.115729 restraints weight = 25599.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.117568 restraints weight = 23481.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  15920  Z= 0.108
  Angle     :  0.502  12.528  21657  Z= 0.254
  Chirality :  0.036   0.149   2651
  Planarity :  0.004   0.078   2627
  Dihedral  :  7.414  82.607   2887
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 26.72 %
    Favored  : 70.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.19), residues: 1947
  helix:  2.41 (0.14), residues: 1404
  sheet:  1.05 (0.49), residues: 98
  loop : -1.21 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 635 
 HIS   0.004   0.000   HIS A1120 
 PHE   0.009   0.001   PHE B 575 
 TYR   0.016   0.001   TYR B 309 
 ARG   0.002   0.000   ARG A 856 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04470 ( 1106)
  hydrogen bonds       : angle       3.43476 ( 3273)
  covalent geometry    : bond        0.00222 (15920)
  covalent geometry    : angle       0.50194 (21657)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 143
  time to evaluate  : 1.599 
Fit side-chains
REVERT: A  199 MET cc_start: 0.8543 (mmm) cc_final: 0.8053 (tpp)
REVERT: A  512 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9054 (tp)
REVERT: A  586 MET cc_start: 0.7483 (ttm) cc_final: 0.7159 (ttt)
REVERT: B  199 MET cc_start: 0.8437 (mmm) cc_final: 0.8086 (tpp)
REVERT: B  295 ASN cc_start: 0.7553 (t0) cc_final: 0.7305 (t0)
REVERT: B  451 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7333 (mm)
  outliers start: 48
  outliers final: 26
  residues processed: 186
  average time/residue: 0.2235
  time to fit residues: 67.1757
Evaluate side-chains
  163 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 1.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  172 PHE
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  878 VAL
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1167 ILE
Chi-restraints excluded: chain B residue  268 PHE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  837 TYR
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  941 LEU
Chi-restraints excluded: chain B residue  989 VAL
Chi-restraints excluded: chain B residue 1081 THR
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1167 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 135 optimal weight:    4.9990
   chunk 70 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   chunk 163 optimal weight:    4.9990
   chunk 160 optimal weight:   10.0000
   chunk 62 optimal weight:    0.0670
   chunk 131 optimal weight:    6.9990
   chunk 134 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   chunk 141 optimal weight:    1.9990
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
A1120 HIS
** B1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.151263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.116696 restraints weight = 25454.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.115601 restraints weight = 26703.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.117514 restraints weight = 22251.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  15920  Z= 0.107
  Angle     :  0.491   9.439  21657  Z= 0.250
  Chirality :  0.036   0.159   2651
  Planarity :  0.003   0.079   2627
  Dihedral  :  7.170  83.759   2887
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 25.47 %
    Favored  : 70.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.19), residues: 1947
  helix:  2.49 (0.14), residues: 1403
  sheet:  1.06 (0.50), residues: 98
  loop : -1.17 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 635 
 HIS   0.005   0.000   HIS A1120 
 PHE   0.007   0.001   PHE A 575 
 TYR   0.016   0.001   TYR B 309 
 ARG   0.003   0.000   ARG A 573 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04283 ( 1106)
  hydrogen bonds       : angle       3.37619 ( 3273)
  covalent geometry    : bond        0.00222 (15920)
  covalent geometry    : angle       0.49093 (21657)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 145
  time to evaluate  : 1.817 
Fit side-chains
REVERT: A  152 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8998 (t80)
REVERT: A  199 MET cc_start: 0.8524 (mmm) cc_final: 0.8112 (tpp)
REVERT: A  512 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9028 (tp)
REVERT: B  152 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.9032 (t80)
REVERT: B  199 MET cc_start: 0.8432 (mmm) cc_final: 0.8130 (tpp)
REVERT: B  295 ASN cc_start: 0.7547 (t0) cc_final: 0.7289 (t0)
REVERT: B  451 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7394 (mm)
REVERT: B  512 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8989 (tp)
  outliers start: 63
  outliers final: 34
  residues processed: 199
  average time/residue: 0.2332
  time to fit residues: 74.5397
Evaluate side-chains
  173 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 134
  time to evaluate  : 1.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  152 PHE
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  172 PHE
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  878 VAL
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1167 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  152 PHE
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  268 PHE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  837 TYR
Chi-restraints excluded: chain B residue  878 VAL
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  941 LEU
Chi-restraints excluded: chain B residue  969 LEU
Chi-restraints excluded: chain B residue  989 VAL
Chi-restraints excluded: chain B residue 1081 THR
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1167 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 110 optimal weight:    0.6980
   chunk 34 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 185 optimal weight:   10.0000
   chunk 81 optimal weight:    4.9990
   chunk 164 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 139 optimal weight:    0.0770
   chunk 179 optimal weight:    1.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1120 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.152050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.117639 restraints weight = 25340.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.116640 restraints weight = 26510.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.118569 restraints weight = 22260.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.1328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  15920  Z= 0.101
  Angle     :  0.486   9.947  21657  Z= 0.245
  Chirality :  0.036   0.171   2651
  Planarity :  0.003   0.079   2627
  Dihedral  :  6.893  85.212   2887
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 26.10 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.55 (0.20), residues: 1947
  helix:  2.55 (0.14), residues: 1404
  sheet:  1.23 (0.50), residues: 96
  loop : -1.16 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 635 
 HIS   0.004   0.000   HIS A1120 
 PHE   0.008   0.001   PHE B 598 
 TYR   0.015   0.001   TYR A 312 
 ARG   0.002   0.000   ARG A 573 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04052 ( 1106)
  hydrogen bonds       : angle       3.30827 ( 3273)
  covalent geometry    : bond        0.00207 (15920)
  covalent geometry    : angle       0.48594 (21657)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 146
  time to evaluate  : 1.745 
Fit side-chains
REVERT: A  152 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.9011 (t80)
REVERT: A  199 MET cc_start: 0.8480 (mmm) cc_final: 0.8026 (tpp)
REVERT: A  295 ASN cc_start: 0.7432 (t0) cc_final: 0.7161 (t0)
REVERT: A  512 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9012 (tp)
REVERT: A  979 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6004 (tt)
REVERT: B  152 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.9024 (t80)
REVERT: B  199 MET cc_start: 0.8425 (mmm) cc_final: 0.8110 (tpp)
REVERT: B  295 ASN cc_start: 0.7547 (t0) cc_final: 0.7278 (t0)
REVERT: B  451 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7352 (mm)
REVERT: B  512 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8973 (tp)
REVERT: B  979 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.5958 (tt)
  outliers start: 56
  outliers final: 32
  residues processed: 196
  average time/residue: 0.2272
  time to fit residues: 71.7225
Evaluate side-chains
  179 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 140
  time to evaluate  : 1.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  152 PHE
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  878 VAL
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1061 THR
Chi-restraints excluded: chain A residue 1073 MET
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1167 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  152 PHE
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  268 PHE
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  575 PHE
Chi-restraints excluded: chain B residue  837 TYR
Chi-restraints excluded: chain B residue  878 VAL
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  941 LEU
Chi-restraints excluded: chain B residue  969 LEU
Chi-restraints excluded: chain B residue  979 LEU
Chi-restraints excluded: chain B residue 1061 THR
Chi-restraints excluded: chain B residue 1081 THR
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1167 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 131 optimal weight:    9.9990
   chunk 59 optimal weight:   10.0000
   chunk 95 optimal weight:    7.9990
   chunk 116 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 174 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 179 optimal weight:    5.9990
   chunk 87 optimal weight:    0.6980
   chunk 185 optimal weight:    9.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.149329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.115629 restraints weight = 25392.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.114745 restraints weight = 27000.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.116159 restraints weight = 24058.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15920  Z= 0.130
  Angle     :  0.523  10.912  21657  Z= 0.263
  Chirality :  0.037   0.166   2651
  Planarity :  0.004   0.079   2627
  Dihedral  :  7.004  84.528   2887
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 26.91 %
    Favored  : 69.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.20), residues: 1947
  helix:  2.52 (0.14), residues: 1402
  sheet:  1.42 (0.51), residues: 94
  loop : -1.24 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 962 
 HIS   0.002   0.000   HIS B1120 
 PHE   0.010   0.001   PHE A 248 
 TYR   0.022   0.001   TYR B 309 
 ARG   0.002   0.000   ARG B 573 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04704 ( 1106)
  hydrogen bonds       : angle       3.39670 ( 3273)
  covalent geometry    : bond        0.00297 (15920)
  covalent geometry    : angle       0.52261 (21657)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 138
  time to evaluate  : 1.649 
Fit side-chains
REVERT: A  152 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.8997 (t80)
REVERT: A  199 MET cc_start: 0.8536 (mmm) cc_final: 0.8246 (tpp)
REVERT: A  295 ASN cc_start: 0.7539 (t0) cc_final: 0.7290 (t0)
REVERT: A  512 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9007 (tp)
REVERT: A  979 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6184 (tt)
REVERT: B  152 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.9064 (t80)
REVERT: B  199 MET cc_start: 0.8476 (mmm) cc_final: 0.8187 (tpp)
REVERT: B  295 ASN cc_start: 0.7592 (t0) cc_final: 0.7369 (t0)
REVERT: B  451 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7546 (mm)
REVERT: B  512 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9028 (tp)
REVERT: B  584 LEU cc_start: 0.8543 (mm) cc_final: 0.8218 (mm)
REVERT: B  625 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.6822 (m-80)
REVERT: B  979 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6092 (tt)
  outliers start: 58
  outliers final: 39
  residues processed: 189
  average time/residue: 0.2253
  time to fit residues: 68.3232
Evaluate side-chains
  182 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 135
  time to evaluate  : 1.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  152 PHE
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  878 VAL
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1073 MET
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1167 ILE
Chi-restraints excluded: chain A residue 1189 VAL
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  152 PHE
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  268 PHE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  575 PHE
Chi-restraints excluded: chain B residue  625 PHE
Chi-restraints excluded: chain B residue  626 ILE
Chi-restraints excluded: chain B residue  837 TYR
Chi-restraints excluded: chain B residue  878 VAL
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  909 SER
Chi-restraints excluded: chain B residue  941 LEU
Chi-restraints excluded: chain B residue  969 LEU
Chi-restraints excluded: chain B residue  979 LEU
Chi-restraints excluded: chain B residue 1073 MET
Chi-restraints excluded: chain B residue 1081 THR
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1167 ILE
Chi-restraints excluded: chain B residue 1189 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 139 optimal weight:    1.9990
   chunk 195 optimal weight:   10.0000
   chunk 125 optimal weight:    0.6980
   chunk 103 optimal weight:    4.9990
   chunk 95 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 54 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.149543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.115665 restraints weight = 25088.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.115158 restraints weight = 24594.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.116749 restraints weight = 23175.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15920  Z= 0.126
  Angle     :  0.527  11.402  21657  Z= 0.265
  Chirality :  0.037   0.184   2651
  Planarity :  0.003   0.079   2627
  Dihedral  :  6.914  84.786   2887
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 27.03 %
    Favored  : 69.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.50 (0.19), residues: 1947
  helix:  2.52 (0.14), residues: 1405
  sheet:  1.47 (0.51), residues: 94
  loop : -1.25 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 419 
 HIS   0.002   0.000   HIS A1120 
 PHE   0.009   0.001   PHE A 195 
 TYR   0.021   0.001   TYR B 309 
 ARG   0.001   0.000   ARG B 573 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04652 ( 1106)
  hydrogen bonds       : angle       3.38873 ( 3273)
  covalent geometry    : bond        0.00287 (15920)
  covalent geometry    : angle       0.52737 (21657)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 143
  time to evaluate  : 1.839 
Fit side-chains
REVERT: A  152 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.8983 (t80)
REVERT: A  199 MET cc_start: 0.8545 (mmm) cc_final: 0.8238 (tpp)
REVERT: A  295 ASN cc_start: 0.7510 (t0) cc_final: 0.7258 (t0)
REVERT: A  512 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8954 (tp)
REVERT: A  848 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6345 (tt0)
REVERT: A  979 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6232 (tt)
REVERT: B  199 MET cc_start: 0.8458 (mmm) cc_final: 0.8202 (tpp)
REVERT: B  295 ASN cc_start: 0.7614 (t0) cc_final: 0.7378 (t0)
REVERT: B  451 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7412 (mm)
REVERT: B  512 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8990 (tp)
REVERT: B  584 LEU cc_start: 0.8531 (mm) cc_final: 0.8231 (mm)
REVERT: B  625 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6822 (m-80)
REVERT: B  979 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6147 (tt)
  outliers start: 59
  outliers final: 42
  residues processed: 196
  average time/residue: 0.2659
  time to fit residues: 85.6091
Evaluate side-chains
  189 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 139
  time to evaluate  : 1.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  152 PHE
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  848 GLU
Chi-restraints excluded: chain A residue  878 VAL
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  936 ILE
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1167 ILE
Chi-restraints excluded: chain A residue 1189 VAL
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  268 PHE
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  575 PHE
Chi-restraints excluded: chain B residue  625 PHE
Chi-restraints excluded: chain B residue  626 ILE
Chi-restraints excluded: chain B residue  837 TYR
Chi-restraints excluded: chain B residue  878 VAL
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  936 ILE
Chi-restraints excluded: chain B residue  941 LEU
Chi-restraints excluded: chain B residue  969 LEU
Chi-restraints excluded: chain B residue  973 ILE
Chi-restraints excluded: chain B residue  979 LEU
Chi-restraints excluded: chain B residue 1061 THR
Chi-restraints excluded: chain B residue 1081 THR
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1167 ILE
Chi-restraints excluded: chain B residue 1189 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 158 optimal weight:   50.0000
   chunk 47 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 174 optimal weight:    8.9990
   chunk 123 optimal weight:    0.7980
   chunk 33 optimal weight:    6.9990
   chunk 112 optimal weight:    6.9990
   chunk 141 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 14 optimal weight:    8.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 830 ASN
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.144520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.110514 restraints weight = 25510.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.110889 restraints weight = 26312.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.112570 restraints weight = 24448.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  15920  Z= 0.237
  Angle     :  0.654  11.318  21657  Z= 0.329
  Chirality :  0.041   0.205   2651
  Planarity :  0.004   0.079   2627
  Dihedral  :  7.552  82.172   2887
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 26.78 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.19), residues: 1947
  helix:  2.15 (0.14), residues: 1411
  sheet:  1.34 (0.49), residues: 94
  loop : -1.41 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 595 
 HIS   0.003   0.001   HIS B 126 
 PHE   0.016   0.002   PHE A 195 
 TYR   0.027   0.002   TYR B 309 
 ARG   0.003   0.000   ARG A 899 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06363 ( 1106)
  hydrogen bonds       : angle       3.75465 ( 3273)
  covalent geometry    : bond        0.00581 (15920)
  covalent geometry    : angle       0.65439 (21657)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 138
  time to evaluate  : 1.814 
Fit side-chains
REVERT: A  199 MET cc_start: 0.8603 (mmm) cc_final: 0.8203 (tpp)
REVERT: A  512 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9067 (tp)
REVERT: A  678 MET cc_start: 0.5420 (ppp) cc_final: 0.5111 (ppp)
REVERT: A  848 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6495 (tt0)
REVERT: A  872 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7731 (pp20)
REVERT: A  979 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6324 (tt)
REVERT: B  300 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7135 (mt-10)
REVERT: B  451 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7621 (mm)
REVERT: B  512 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9051 (tp)
REVERT: B  584 LEU cc_start: 0.8548 (mm) cc_final: 0.8235 (mm)
REVERT: B  625 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.7060 (m-80)
REVERT: B  848 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6476 (tt0)
REVERT: B  872 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7786 (pp20)
REVERT: B  979 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6251 (tt)
  outliers start: 64
  outliers final: 47
  residues processed: 197
  average time/residue: 0.2340
  time to fit residues: 73.3847
Evaluate side-chains
  187 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 129
  time to evaluate  : 1.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  848 GLU
Chi-restraints excluded: chain A residue  872 GLU
Chi-restraints excluded: chain A residue  878 VAL
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  936 ILE
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1167 ILE
Chi-restraints excluded: chain A residue 1189 VAL
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  268 PHE
Chi-restraints excluded: chain B residue  300 GLU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  575 PHE
Chi-restraints excluded: chain B residue  625 PHE
Chi-restraints excluded: chain B residue  626 ILE
Chi-restraints excluded: chain B residue  837 TYR
Chi-restraints excluded: chain B residue  848 GLU
Chi-restraints excluded: chain B residue  872 GLU
Chi-restraints excluded: chain B residue  878 VAL
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  909 SER
Chi-restraints excluded: chain B residue  936 ILE
Chi-restraints excluded: chain B residue  941 LEU
Chi-restraints excluded: chain B residue  969 LEU
Chi-restraints excluded: chain B residue  973 ILE
Chi-restraints excluded: chain B residue  978 SER
Chi-restraints excluded: chain B residue  979 LEU
Chi-restraints excluded: chain B residue 1081 THR
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1167 ILE
Chi-restraints excluded: chain B residue 1189 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 184 optimal weight:    3.9990
   chunk 142 optimal weight:    0.7980
   chunk 117 optimal weight:    2.9990
   chunk 124 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 177 optimal weight:    7.9990
   chunk 77 optimal weight:    0.1980
   chunk 12 optimal weight:    0.7980
   chunk 163 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0570
   chunk 132 optimal weight:    2.9990
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
A1120 HIS
** B1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.150227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.116343 restraints weight = 25217.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.116650 restraints weight = 25410.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.118446 restraints weight = 23175.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  15920  Z= 0.112
  Angle     :  0.537  12.254  21657  Z= 0.271
  Chirality :  0.037   0.210   2651
  Planarity :  0.004   0.082   2627
  Dihedral  :  6.838  87.261   2887
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 28.66 %
    Favored  : 68.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.19), residues: 1947
  helix:  2.48 (0.14), residues: 1404
  sheet:  0.74 (0.47), residues: 124
  loop : -1.15 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 962 
 HIS   0.003   0.001   HIS A1120 
 PHE   0.027   0.001   PHE B 625 
 TYR   0.016   0.001   TYR B 309 
 ARG   0.002   0.000   ARG B 865 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04548 ( 1106)
  hydrogen bonds       : angle       3.41430 ( 3273)
  covalent geometry    : bond        0.00232 (15920)
  covalent geometry    : angle       0.53703 (21657)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 141
  time to evaluate  : 1.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 MET cc_start: 0.8507 (mmm) cc_final: 0.8175 (tpp)
REVERT: A  512 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9027 (tp)
REVERT: A  678 MET cc_start: 0.5328 (ppp) cc_final: 0.5043 (ppp)
REVERT: A  942 MET cc_start: 0.7969 (tpt) cc_final: 0.7532 (tpp)
REVERT: A  979 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6152 (tt)
REVERT: B  199 MET cc_start: 0.8428 (mmm) cc_final: 0.8126 (tpp)
REVERT: B  512 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8973 (tp)
REVERT: B  584 LEU cc_start: 0.8435 (mm) cc_final: 0.8160 (mm)
REVERT: B  942 MET cc_start: 0.7932 (tpt) cc_final: 0.7474 (tpp)
REVERT: B  979 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6116 (tt)
  outliers start: 39
  outliers final: 33
  residues processed: 176
  average time/residue: 0.2871
  time to fit residues: 79.6039
Evaluate side-chains
  174 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 137
  time to evaluate  : 1.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1167 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  268 PHE
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  575 PHE
Chi-restraints excluded: chain B residue  837 TYR
Chi-restraints excluded: chain B residue  909 SER
Chi-restraints excluded: chain B residue  941 LEU
Chi-restraints excluded: chain B residue  969 LEU
Chi-restraints excluded: chain B residue  973 ILE
Chi-restraints excluded: chain B residue  979 LEU
Chi-restraints excluded: chain B residue 1061 THR
Chi-restraints excluded: chain B residue 1081 THR
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1167 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 114 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   chunk 168 optimal weight:    3.9990
   chunk 190 optimal weight:    0.8980
   chunk 93 optimal weight:    9.9990
   chunk 106 optimal weight:    3.9990
   chunk 143 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9980
   chunk 126 optimal weight:    0.6980
   chunk 80 optimal weight:    9.9990
   chunk 188 optimal weight:    0.3980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.150109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.116565 restraints weight = 25345.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.115622 restraints weight = 25696.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.117115 restraints weight = 23806.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  15920  Z= 0.113
  Angle     :  0.534  11.865  21657  Z= 0.267
  Chirality :  0.037   0.211   2651
  Planarity :  0.003   0.080   2627
  Dihedral  :  6.769  85.136   2887
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 28.97 %
    Favored  : 68.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.19), residues: 1947
  helix:  2.53 (0.14), residues: 1404
  sheet:  1.01 (0.49), residues: 110
  loop : -1.19 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 635 
 HIS   0.003   0.000   HIS A1120 
 PHE   0.007   0.001   PHE A 248 
 TYR   0.018   0.001   TYR B 309 
 ARG   0.002   0.000   ARG B 585 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04422 ( 1106)
  hydrogen bonds       : angle       3.35945 ( 3273)
  covalent geometry    : bond        0.00245 (15920)
  covalent geometry    : angle       0.53376 (21657)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4709.20 seconds
wall clock time: 85 minutes 45.51 seconds (5145.51 seconds total)