Starting phenix.real_space_refine
on Wed May 14 04:40:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jpo_36485/05_2025/8jpo_36485.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jpo_36485/05_2025/8jpo_36485.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jpo_36485/05_2025/8jpo_36485.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jpo_36485/05_2025/8jpo_36485.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jpo_36485/05_2025/8jpo_36485.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jpo_36485/05_2025/8jpo_36485.cif"
  }
  resolution = 3.4
  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=   0.001 sd=   0.004
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: 7
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      70      5.16       5
     Cl      4      4.86       5
     C    7430      2.51       5
     N    1922      2.21       5
     O    2042      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11476
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 733, 5704
          Classifications: {'peptide': 733}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 31, 'TRANS': 701}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 40
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "B"
      Number of atoms: 5704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 733, 5704
          Classifications: {'peptide': 733}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 31, 'TRANS': 701}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 40
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 34
          Unusual residues: {' CL': 2, ' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 34
          Unusual residues: {' CL': 2, ' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 7.09, per 1000 atoms: 0.62
  Number of scatterers: 11476
  At special positions: 0
  Unit cell: (92.9514, 96.301, 113.886, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Cl      4     17.00
     S      70     16.00
     P       6     15.00
     Mg      2     11.99
     O    2042      8.00
     N    1922      7.00
     C    7430      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 120 " - pdb=" SG  CYS A 125 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 319 " - pdb=" SG  CYS A 326 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 399 " - pdb=" SG  CYS A 430 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 120 " - pdb=" SG  CYS B 125 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 319 " - pdb=" SG  CYS B 326 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 399 " - pdb=" SG  CYS B 430 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.70
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2696

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 8 sheets defined
      65.4% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 68
    Processing helix  chain 'A' and resid 69 through 123
      removed outlier: 3.554A  pdb=" N   LEU A 108 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   THR A 115 " --> pdb=" O   GLY A 111 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   SER A 116 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 151
      removed outlier: 3.605A  pdb=" N   VAL A 148 " --> pdb=" O   ALA A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 155
    Processing helix  chain 'A' and resid 158 through 160
      No H-bonds generated for 'chain 'A' and resid 158 through 160'
    Processing helix  chain 'A' and resid 161 through 166
      removed outlier: 3.825A  pdb=" N   TYR A 165 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 191
      removed outlier: 3.618A  pdb=" N   GLY A 186 " --> pdb=" O   CYS A 182 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU A 188 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   PHE A 189 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 194
      No H-bonds generated for 'chain 'A' and resid 192 through 194'
    Processing helix  chain 'A' and resid 201 through 214
      removed outlier: 4.341A  pdb=" N   HIS A 205 " --> pdb=" O   GLY A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 233
      removed outlier: 3.549A  pdb=" N   PHE A 232 " --> pdb=" O   PHE A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 255
      removed outlier: 4.087A  pdb=" N   ASP A 240 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 266
    Processing helix  chain 'A' and resid 276 through 299
      removed outlier: 3.681A  pdb=" N   PHE A 282 " --> pdb=" O   TRP A 278 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASN A 292 " --> pdb=" O   THR A 288 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   PHE A 293 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY A 297 " --> pdb=" O   PHE A 293 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   GLN A 299 " --> pdb=" O   ARG A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 366
      removed outlier: 4.217A  pdb=" N   PHE A 336 " --> pdb=" O   MET A 332 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ARG A 364 " --> pdb=" O   LYS A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 395
    Processing helix  chain 'A' and resid 437 through 443
    Processing helix  chain 'A' and resid 445 through 456
    Processing helix  chain 'A' and resid 461 through 480
    Processing helix  chain 'A' and resid 488 through 511
      removed outlier: 3.760A  pdb=" N   CYS A 495 " --> pdb=" O   PRO A 491 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLY A 496 " --> pdb=" O   SER A 492 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ALA A 497 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 534
      removed outlier: 3.816A  pdb=" N   ALA A 522 " --> pdb=" O   SER A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 549
    Processing helix  chain 'A' and resid 550 through 552
      No H-bonds generated for 'chain 'A' and resid 550 through 552'
    Processing helix  chain 'A' and resid 553 through 569
      removed outlier: 3.852A  pdb=" N   VAL A 563 " --> pdb=" O   VAL A 559 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA A 564 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   TRP A 566 " --> pdb=" O   MET A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 582
    Processing helix  chain 'A' and resid 593 through 598
    Processing helix  chain 'A' and resid 600 through 605
      removed outlier: 3.793A  pdb=" N   ILE A 604 " --> pdb=" O   ARG A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 628
    Processing helix  chain 'A' and resid 650 through 664
      removed outlier: 3.605A  pdb=" N   ILE A 664 " --> pdb=" O   LYS A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 677
    Processing helix  chain 'A' and resid 732 through 736
    Processing helix  chain 'A' and resid 747 through 756
    Processing helix  chain 'A' and resid 773 through 779
    Processing helix  chain 'A' and resid 819 through 830
    Processing helix  chain 'A' and resid 849 through 853
    Processing helix  chain 'A' and resid 854 through 869
    Processing helix  chain 'B' and resid 58 through 68
    Processing helix  chain 'B' and resid 69 through 123
      removed outlier: 3.648A  pdb=" N   VAL B 113 " --> pdb=" O   LYS B 109 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   THR B 115 " --> pdb=" O   GLY B 111 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   SER B 116 " --> pdb=" O   VAL B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 151
      removed outlier: 3.600A  pdb=" N   VAL B 148 " --> pdb=" O   ALA B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 155
    Processing helix  chain 'B' and resid 158 through 160
      No H-bonds generated for 'chain 'B' and resid 158 through 160'
    Processing helix  chain 'B' and resid 161 through 166
      removed outlier: 3.832A  pdb=" N   TYR B 165 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 191
      removed outlier: 3.623A  pdb=" N   GLY B 186 " --> pdb=" O   CYS B 182 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU B 188 " --> pdb=" O   VAL B 184 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   PHE B 189 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 194
      No H-bonds generated for 'chain 'B' and resid 192 through 194'
    Processing helix  chain 'B' and resid 199 through 214
      removed outlier: 3.558A  pdb=" N   MET B 203 " --> pdb=" O   LYS B 199 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ILE B 204 " --> pdb=" O   GLU B 200 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   HIS B 205 " --> pdb=" O   GLY B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 233
      removed outlier: 3.527A  pdb=" N   PHE B 232 " --> pdb=" O   PHE B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 255
      removed outlier: 4.067A  pdb=" N   ASP B 240 " --> pdb=" O   ARG B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 266
    Processing helix  chain 'B' and resid 276 through 299
      removed outlier: 3.668A  pdb=" N   PHE B 282 " --> pdb=" O   TRP B 278 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASN B 292 " --> pdb=" O   THR B 288 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE B 293 " --> pdb=" O   PHE B 289 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY B 297 " --> pdb=" O   PHE B 293 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLN B 299 " --> pdb=" O   ARG B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 366
      removed outlier: 4.152A  pdb=" N   PHE B 336 " --> pdb=" O   MET B 332 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ARG B 364 " --> pdb=" O   LYS B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 395
      removed outlier: 3.636A  pdb=" N   VAL B 389 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 437 through 443
    Processing helix  chain 'B' and resid 445 through 456
      removed outlier: 3.650A  pdb=" N   GLN B 456 " --> pdb=" O   GLN B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 480
    Processing helix  chain 'B' and resid 488 through 511
      removed outlier: 3.751A  pdb=" N   CYS B 495 " --> pdb=" O   PRO B 491 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLY B 496 " --> pdb=" O   SER B 492 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ALA B 497 " --> pdb=" O   LEU B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 534
      removed outlier: 3.904A  pdb=" N   ALA B 522 " --> pdb=" O   SER B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 549
    Processing helix  chain 'B' and resid 550 through 552
      No H-bonds generated for 'chain 'B' and resid 550 through 552'
    Processing helix  chain 'B' and resid 553 through 569
      removed outlier: 3.811A  pdb=" N   VAL B 563 " --> pdb=" O   VAL B 559 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ALA B 564 " --> pdb=" O   THR B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 582
    Processing helix  chain 'B' and resid 593 through 598
    Processing helix  chain 'B' and resid 600 through 605
      removed outlier: 3.800A  pdb=" N   ILE B 604 " --> pdb=" O   ARG B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 618 through 628
    Processing helix  chain 'B' and resid 650 through 664
      removed outlier: 3.658A  pdb=" N   ILE B 664 " --> pdb=" O   LYS B 660 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 677
    Processing helix  chain 'B' and resid 732 through 736
    Processing helix  chain 'B' and resid 747 through 756
    Processing helix  chain 'B' and resid 773 through 779
    Processing helix  chain 'B' and resid 819 through 830
    Processing helix  chain 'B' and resid 854 through 869
    Processing sheet with id=AA1, first strand: chain 'A' and resid 399 through 401
    Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 617
    Processing sheet with id=AA3, first strand: chain 'A' and resid 632 through 638
      removed outlier: 6.546A  pdb=" N   THR A 637 " --> pdb=" O   PHE A 741 " (cutoff:3.500A)
      removed outlier: 5.557A  pdb=" N   PHE A 741 " --> pdb=" O   THR A 637 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 835 through 838
      removed outlier: 6.808A  pdb=" N   LEU A 835 " --> pdb=" O   ILE A 847 " (cutoff:3.500A)
      removed outlier: 4.863A  pdb=" N   ILE A 847 " --> pdb=" O   LEU A 835 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   VAL A 837 " --> pdb=" O   VAL A 845 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 399 through 401
    Processing sheet with id=AA6, first strand: chain 'B' and resid 616 through 617
    Processing sheet with id=AA7, first strand: chain 'B' and resid 632 through 638
      removed outlier: 6.546A  pdb=" N   THR B 637 " --> pdb=" O   PHE B 741 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   PHE B 741 " --> pdb=" O   THR B 637 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 835 through 838
      removed outlier: 6.782A  pdb=" N   LEU B 835 " --> pdb=" O   ILE B 847 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ILE B 847 " --> pdb=" O   LEU B 835 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   VAL B 837 " --> pdb=" O   VAL B 845 " (cutoff:3.500A)

    655 hydrogen bonds defined for protein.
    1941 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.28

  Time building geometry restraints manager: 3.16 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3614
        1.34 -     1.47: 2886
        1.47 -     1.59: 5122
        1.59 -     1.71: 2
        1.71 -     1.83: 110
  Bond restraints: 11734
  Sorted by residual:
  bond pdb=" C   HIS B 367 "
       pdb=" N   PRO B 368 "
    ideal  model  delta    sigma   weight residual
    1.334  1.371 -0.037 2.34e-02 1.83e+03 2.54e+00
  bond pdb=" C   HIS A 367 "
       pdb=" N   PRO A 368 "
    ideal  model  delta    sigma   weight residual
    1.334  1.370 -0.036 2.34e-02 1.83e+03 2.42e+00
  bond pdb=" CA  GLY B 397 "
       pdb=" C   GLY B 397 "
    ideal  model  delta    sigma   weight residual
    1.520  1.512  0.008 7.30e-03 1.88e+04 1.29e+00
  bond pdb=" C   VAL A 175 "
       pdb=" O   VAL A 175 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.013 1.19e-02 7.06e+03 1.16e+00
  bond pdb=" CA  GLY A 397 "
       pdb=" C   GLY A 397 "
    ideal  model  delta    sigma   weight residual
    1.520  1.512  0.008 7.30e-03 1.88e+04 1.13e+00
  ... (remaining 11729 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 15186
        1.28 -     2.56: 586
        2.56 -     3.84: 117
        3.84 -     5.12: 30
        5.12 -     6.40: 9
  Bond angle restraints: 15928
  Sorted by residual:
  angle pdb=" N   VAL A 162 "
        pdb=" CA  VAL A 162 "
        pdb=" C   VAL A 162 "
      ideal   model   delta    sigma   weight residual
     112.96  107.99    4.97 1.00e+00 1.00e+00 2.47e+01
  angle pdb=" N   VAL B 162 "
        pdb=" CA  VAL B 162 "
        pdb=" C   VAL B 162 "
      ideal   model   delta    sigma   weight residual
     112.96  108.09    4.87 1.00e+00 1.00e+00 2.37e+01
  angle pdb=" C   GLY A 158 "
        pdb=" N   ILE A 159 "
        pdb=" CA  ILE A 159 "
      ideal   model   delta    sigma   weight residual
     120.24  122.96   -2.72 6.30e-01 2.52e+00 1.86e+01
  angle pdb=" C   GLY B 158 "
        pdb=" N   ILE B 159 "
        pdb=" CA  ILE B 159 "
      ideal   model   delta    sigma   weight residual
     120.24  122.94   -2.70 6.30e-01 2.52e+00 1.83e+01
  angle pdb=" C   ILE A 159 "
        pdb=" CA  ILE A 159 "
        pdb=" CB  ILE A 159 "
      ideal   model   delta    sigma   weight residual
     114.35  110.96    3.39 1.06e+00 8.90e-01 1.02e+01
  ... (remaining 15923 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.64: 6212
       14.64 -    29.27: 527
       29.27 -    43.91: 140
       43.91 -    58.55: 46
       58.55 -    73.19: 21
  Dihedral angle restraints: 6946
    sinusoidal: 2748
      harmonic: 4198
  Sorted by residual:
  dihedral pdb=" CB  CYS A 120 "
           pdb=" SG  CYS A 120 "
           pdb=" SG  CYS A 125 "
           pdb=" CB  CYS A 125 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -148.19   62.19     1      1.00e+01 1.00e-02 5.12e+01
  dihedral pdb=" CB  CYS B 120 "
           pdb=" SG  CYS B 120 "
           pdb=" SG  CYS B 125 "
           pdb=" CB  CYS B 125 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.05   61.05     1      1.00e+01 1.00e-02 4.95e+01
  dihedral pdb=" CA  VAL A 171 "
           pdb=" C   VAL A 171 "
           pdb=" N   PRO A 172 "
           pdb=" CA  PRO A 172 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.64  -21.36     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 6943 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1173
       0.032 -    0.064: 466
       0.064 -    0.096: 132
       0.096 -    0.128: 64
       0.128 -    0.160: 7
  Chirality restraints: 1842
  Sorted by residual:
  chirality pdb=" CA  VAL A 171 "
            pdb=" N   VAL A 171 "
            pdb=" C   VAL A 171 "
            pdb=" CB  VAL A 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.44e-01
  chirality pdb=" CA  VAL B 171 "
            pdb=" N   VAL B 171 "
            pdb=" C   VAL B 171 "
            pdb=" CB  VAL B 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.19e-01
  chirality pdb=" CB  VAL B 242 "
            pdb=" CA  VAL B 242 "
            pdb=" CG1 VAL B 242 "
            pdb=" CG2 VAL B 242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.86e-01
  ... (remaining 1839 not shown)

  Planarity restraints: 1990
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 769 "   -0.027 5.00e-02 4.00e+02   4.04e-02 2.61e+00
        pdb=" N   PRO A 770 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 770 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 770 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 769 "    0.026 5.00e-02 4.00e+02   3.98e-02 2.53e+00
        pdb=" N   PRO B 770 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 770 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 770 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 484 "    0.026 5.00e-02 4.00e+02   3.94e-02 2.48e+00
        pdb=" N   PRO B 485 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 485 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 485 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1987 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 2824
        2.79 -     3.32: 11215
        3.32 -     3.85: 18893
        3.85 -     4.37: 22316
        4.37 -     4.90: 39182
  Nonbonded interactions: 94430
  Sorted by model distance:
  nonbonded pdb=" O   THR B 440 "
            pdb=" ND2 ASN B 444 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" O   ASP A 603 "
            pdb=" NH1 ARG A 861 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" O   ASP B 603 "
            pdb=" NH1 ARG B 861 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" O   THR A 440 "
            pdb=" ND2 ASN A 444 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" O   PRO B 431 "
            pdb=" OG1 THR B 434 "
     model   vdw
     2.308 3.040
  ... (remaining 94425 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: 0.05
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 46 through 869 or resid 902 or resid 904))
  selection = (chain 'B' and (resid 46 through 869 or resid 902 or resid 904))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.680
  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:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     26.940
  Find NCS groups from input model:        0.530
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
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      :  0.004   0.037  11740  Z= 0.166
  Angle     :  0.630   6.396  15940  Z= 0.373
  Chirality :  0.041   0.160   1842
  Planarity :  0.005   0.040   1990
  Dihedral  : 12.938  73.186   4232
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.23), residues: 1446
  helix:  1.12 (0.18), residues: 896
  sheet: -2.55 (0.85), residues: 24
  loop : -0.96 (0.27), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 478 
 HIS   0.002   0.001   HIS A 851 
 PHE   0.014   0.001   PHE A 390 
 TYR   0.013   0.001   TYR A 781 
 ARG   0.005   0.000   ARG A 626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17280 (  655)
  hydrogen bonds       : angle       6.01244 ( 1941)
  SS BOND              : bond        0.00401 (    6)
  SS BOND              : angle       1.97106 (   12)
  covalent geometry    : bond        0.00375 (11734)
  covalent geometry    : angle       0.62787 (15928)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1955
  time to fit residues: 33.0686
Evaluate side-chains
  92 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 1.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    5.9990
   chunk 110 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 114 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 132 optimal weight:    0.0050
   overall best weight:    1.3800

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 452 GLN
B 764 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.114782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.089508 restraints weight = 13626.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 1.42
r_work: 0.2881 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.0865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11740  Z= 0.138
  Angle     :  0.553   8.196  15940  Z= 0.283
  Chirality :  0.040   0.158   1842
  Planarity :  0.005   0.038   1990
  Dihedral  :  7.754  59.708   1642
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  5.92 %
    Favored  : 93.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.08 (0.23), residues: 1446
  helix:  1.67 (0.18), residues: 902
  sheet: -2.94 (0.80), residues: 24
  loop : -0.80 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 278 
 HIS   0.003   0.001   HIS B 615 
 PHE   0.011   0.001   PHE A 351 
 TYR   0.026   0.001   TYR A 510 
 ARG   0.003   0.000   ARG A 861 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04572 (  655)
  hydrogen bonds       : angle       3.87028 ( 1941)
  SS BOND              : bond        0.00163 (    6)
  SS BOND              : angle       1.01353 (   12)
  covalent geometry    : bond        0.00327 (11734)
  covalent geometry    : angle       0.55294 (15928)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 1.170 
Fit side-chains
REVERT: B   75 ARG cc_start: 0.7392 (ttm170) cc_final: 0.6893 (ttt90)
  outliers start: 5
  outliers final: 1
  residues processed: 108
  average time/residue: 0.2017
  time to fit residues: 33.5922
Evaluate side-chains
  90 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 1.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  117 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 134 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   chunk 79 optimal weight:    5.9990
   chunk 84 optimal weight:    0.1980
   chunk 40 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 125 optimal weight:    6.9990
   chunk 104 optimal weight:    2.9990
   overall best weight:    2.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 137 ASN
** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 ASN
** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 515 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.110430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.085118 restraints weight = 13994.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 1.43
r_work: 0.2821 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2690 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8870
moved from start:          0.1195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  11740  Z= 0.195
  Angle     :  0.577   7.282  15940  Z= 0.296
  Chirality :  0.042   0.158   1842
  Planarity :  0.005   0.041   1990
  Dihedral  :  7.098  53.807   1642
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  7.68 %
    Favored  : 91.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.09 (0.23), residues: 1446
  helix:  1.68 (0.18), residues: 906
  sheet: -2.87 (0.82), residues: 24
  loop : -0.81 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 303 
 HIS   0.003   0.001   HIS B 615 
 PHE   0.015   0.001   PHE A 101 
 TYR   0.017   0.001   TYR A 781 
 ARG   0.002   0.000   ARG B 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04808 (  655)
  hydrogen bonds       : angle       3.81812 ( 1941)
  SS BOND              : bond        0.00218 (    6)
  SS BOND              : angle       0.96583 (   12)
  covalent geometry    : bond        0.00491 (11734)
  covalent geometry    : angle       0.57674 (15928)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 1.411 
Fit side-chains
REVERT: A  120 CYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7562 (t)
REVERT: B  120 CYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7566 (t)
REVERT: B  332 MET cc_start: 0.8212 (mmt) cc_final: 0.7931 (ptm)
  outliers start: 10
  outliers final: 7
  residues processed: 103
  average time/residue: 0.2092
  time to fit residues: 32.9611
Evaluate side-chains
  98 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 1.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain A residue  732 MET
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  120 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 116 optimal weight:    8.9990
   chunk 7 optimal weight:    9.9990
   chunk 82 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 131 optimal weight:   10.0000
   chunk 74 optimal weight:    3.9990
   chunk 130 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 452 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.107387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.081814 restraints weight = 13967.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 1.45
r_work: 0.2819 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8927
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059  11740  Z= 0.264
  Angle     :  0.630   6.515  15940  Z= 0.325
  Chirality :  0.045   0.157   1842
  Planarity :  0.005   0.045   1990
  Dihedral  :  7.299  56.139   1642
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  7.92 %
    Favored  : 90.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.23), residues: 1446
  helix:  1.46 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.04 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 303 
 HIS   0.003   0.001   HIS A 865 
 PHE   0.019   0.002   PHE B 351 
 TYR   0.019   0.002   TYR A 781 
 ARG   0.003   0.000   ARG A 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05319 (  655)
  hydrogen bonds       : angle       3.95598 ( 1941)
  SS BOND              : bond        0.00230 (    6)
  SS BOND              : angle       1.16583 (   12)
  covalent geometry    : bond        0.00672 (11734)
  covalent geometry    : angle       0.62974 (15928)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 1.292 
Fit side-chains
REVERT: A  120 CYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7416 (t)
REVERT: A  266 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8287 (pm20)
REVERT: A  558 MET cc_start: 0.8949 (ttt) cc_final: 0.8729 (ttm)
REVERT: B  120 CYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7516 (t)
REVERT: B  266 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8284 (pm20)
REVERT: B  332 MET cc_start: 0.8363 (mmt) cc_final: 0.8048 (ptm)
  outliers start: 24
  outliers final: 10
  residues processed: 114
  average time/residue: 0.2148
  time to fit residues: 38.4184
Evaluate side-chains
  104 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain A residue  732 MET
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  120 CYS
Chi-restraints excluded: chain B residue  266 GLU
Chi-restraints excluded: chain B residue  732 MET
Chi-restraints excluded: chain B residue  761 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 143 optimal weight:    5.9990
   chunk 141 optimal weight:    0.5980
   chunk 134 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9990
   chunk 110 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 452 GLN
B 456 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.113728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.088426 restraints weight = 13592.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 1.43
r_work: 0.2872 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2741 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8822
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  11740  Z= 0.103
  Angle     :  0.497   7.635  15940  Z= 0.253
  Chirality :  0.038   0.160   1842
  Planarity :  0.004   0.038   1990
  Dihedral  :  6.521  58.216   1642
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  9.52 %
    Favored  : 89.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.29 (0.23), residues: 1446
  helix:  1.97 (0.18), residues: 900
  sheet: -3.08 (0.84), residues: 24
  loop : -0.95 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 278 
 HIS   0.002   0.000   HIS B 615 
 PHE   0.012   0.001   PHE A 101 
 TYR   0.015   0.001   TYR A 781 
 ARG   0.002   0.000   ARG B 861 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03685 (  655)
  hydrogen bonds       : angle       3.63233 ( 1941)
  SS BOND              : bond        0.00079 (    6)
  SS BOND              : angle       0.91223 (   12)
  covalent geometry    : bond        0.00220 (11734)
  covalent geometry    : angle       0.49676 (15928)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 1.282 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 CYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7384 (t)
REVERT: A  360 LYS cc_start: 0.8919 (mttt) cc_final: 0.8634 (mtmm)
REVERT: A  786 ASP cc_start: 0.8215 (t0) cc_final: 0.7924 (t0)
REVERT: B  120 CYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7495 (t)
REVERT: B  332 MET cc_start: 0.8298 (mmt) cc_final: 0.8002 (ptm)
REVERT: B  786 ASP cc_start: 0.8168 (t0) cc_final: 0.7869 (t0)
  outliers start: 15
  outliers final: 6
  residues processed: 115
  average time/residue: 0.1893
  time to fit residues: 34.4292
Evaluate side-chains
  108 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain A residue  732 MET
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  120 CYS
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  427 THR
Chi-restraints excluded: chain B residue  732 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 130 optimal weight:    9.9990
   chunk 144 optimal weight:    0.5980
   chunk 111 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 2 optimal weight:    9.9990
   chunk 70 optimal weight:    0.0000
   chunk 55 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 76 optimal weight:    4.9990
   overall best weight:    2.5190

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

Flipped N/Q/H residues before XYZ refinement:
** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 579 HIS
B 630 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.109336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.083566 restraints weight = 13959.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 1.46
r_work: 0.2800 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8889
moved from start:          0.1627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  11740  Z= 0.197
  Angle     :  0.578   9.124  15940  Z= 0.291
  Chirality :  0.042   0.158   1842
  Planarity :  0.005   0.040   1990
  Dihedral  :  6.867  59.877   1642
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 10.24 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.17 (0.23), residues: 1446
  helix:  1.83 (0.18), residues: 900
  sheet:  None (None), residues: 0
  loop : -1.07 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 303 
 HIS   0.003   0.001   HIS B 615 
 PHE   0.015   0.001   PHE A 351 
 TYR   0.017   0.001   TYR A 781 
 ARG   0.003   0.000   ARG B 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04614 (  655)
  hydrogen bonds       : angle       3.77715 ( 1941)
  SS BOND              : bond        0.00151 (    6)
  SS BOND              : angle       1.06708 (   12)
  covalent geometry    : bond        0.00496 (11734)
  covalent geometry    : angle       0.57792 (15928)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 1.194 
Fit side-chains
REVERT: A  120 CYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7336 (t)
REVERT: A  456 GLN cc_start: 0.7958 (tt0) cc_final: 0.7642 (tt0)
REVERT: A  786 ASP cc_start: 0.8253 (t0) cc_final: 0.7952 (t0)
REVERT: B   75 ARG cc_start: 0.7487 (ttm170) cc_final: 0.6980 (ttt90)
REVERT: B  120 CYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7517 (t)
REVERT: B  332 MET cc_start: 0.8364 (mmt) cc_final: 0.8022 (ptm)
REVERT: B  786 ASP cc_start: 0.8213 (t0) cc_final: 0.7912 (t0)
  outliers start: 15
  outliers final: 7
  residues processed: 107
  average time/residue: 0.1929
  time to fit residues: 32.4384
Evaluate side-chains
  101 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  120 CYS
Chi-restraints excluded: chain B residue  732 MET
Chi-restraints excluded: chain B residue  761 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    1.9990
   chunk 43 optimal weight:    9.9990
   chunk 78 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 104 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A 515 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 = 0.3131 r_free = 0.3131 target = 0.112620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.087082 restraints weight = 13843.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 1.43
r_work: 0.2853 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2724 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8842
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  11740  Z= 0.115
  Angle     :  0.507   8.046  15940  Z= 0.255
  Chirality :  0.038   0.158   1842
  Planarity :  0.004   0.038   1990
  Dihedral  :  6.499  62.623   1642
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.72 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.33 (0.23), residues: 1446
  helix:  2.00 (0.18), residues: 904
  sheet:  None (None), residues: 0
  loop : -1.10 (0.26), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 278 
 HIS   0.002   0.001   HIS B 515 
 PHE   0.012   0.001   PHE A 101 
 TYR   0.015   0.001   TYR A 781 
 ARG   0.002   0.000   ARG B 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03817 (  655)
  hydrogen bonds       : angle       3.63993 ( 1941)
  SS BOND              : bond        0.00086 (    6)
  SS BOND              : angle       0.89733 (   12)
  covalent geometry    : bond        0.00265 (11734)
  covalent geometry    : angle       0.50622 (15928)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 1.179 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 CYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7427 (t)
REVERT: A  570 PHE cc_start: 0.7995 (m-10) cc_final: 0.7769 (t80)
REVERT: A  786 ASP cc_start: 0.8261 (t0) cc_final: 0.7991 (t0)
REVERT: B  120 CYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7514 (t)
REVERT: B  332 MET cc_start: 0.8333 (mmt) cc_final: 0.8024 (ptm)
REVERT: B  570 PHE cc_start: 0.8024 (m-10) cc_final: 0.7770 (t80)
REVERT: B  786 ASP cc_start: 0.8207 (t0) cc_final: 0.7965 (t0)
REVERT: B  850 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8470 (ttm110)
  outliers start: 19
  outliers final: 6
  residues processed: 112
  average time/residue: 0.1947
  time to fit residues: 34.2610
Evaluate side-chains
  105 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  120 CYS
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  427 THR
Chi-restraints excluded: chain B residue  732 MET
Chi-restraints excluded: chain B residue  761 SER
Chi-restraints excluded: chain B residue  850 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 118 optimal weight:    3.9990
   chunk 62 optimal weight:    9.9990
   chunk 70 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 630 HIS
B 579 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.109057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.083244 restraints weight = 13917.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 1.45
r_work: 0.2843 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8905
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  11740  Z= 0.199
  Angle     :  0.578   8.476  15940  Z= 0.290
  Chirality :  0.042   0.198   1842
  Planarity :  0.005   0.040   1990
  Dihedral  :  6.801  59.183   1642
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 11.52 %
    Favored  : 87.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.12 (0.23), residues: 1446
  helix:  1.83 (0.18), residues: 902
  sheet:  None (None), residues: 0
  loop : -1.17 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 303 
 HIS   0.003   0.001   HIS B 579 
 PHE   0.016   0.001   PHE A 351 
 TYR   0.016   0.001   TYR A 781 
 ARG   0.003   0.000   ARG B 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04586 (  655)
  hydrogen bonds       : angle       3.76691 ( 1941)
  SS BOND              : bond        0.00148 (    6)
  SS BOND              : angle       1.03622 (   12)
  covalent geometry    : bond        0.00501 (11734)
  covalent geometry    : angle       0.57709 (15928)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 1.196 
Fit side-chains
REVERT: A  120 CYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7508 (t)
REVERT: A  570 PHE cc_start: 0.8099 (m-10) cc_final: 0.7789 (t80)
REVERT: A  786 ASP cc_start: 0.8302 (t0) cc_final: 0.8032 (t0)
REVERT: B   75 ARG cc_start: 0.7572 (ttm170) cc_final: 0.7014 (ttt90)
REVERT: B  120 CYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7493 (t)
REVERT: B  570 PHE cc_start: 0.8102 (m-10) cc_final: 0.7787 (t80)
REVERT: B  786 ASP cc_start: 0.8218 (t0) cc_final: 0.7934 (t0)
REVERT: B  850 ARG cc_start: 0.9302 (OUTLIER) cc_final: 0.8473 (ttm110)
  outliers start: 17
  outliers final: 6
  residues processed: 111
  average time/residue: 0.1919
  time to fit residues: 33.0573
Evaluate side-chains
  98 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  120 CYS
Chi-restraints excluded: chain B residue  732 MET
Chi-restraints excluded: chain B residue  761 SER
Chi-restraints excluded: chain B residue  850 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 137 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9990
   chunk 97 optimal weight:    7.9990
   chunk 87 optimal weight:    0.8980
   chunk 129 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 796 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.114601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.088894 restraints weight = 13681.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 1.44
r_work: 0.2873 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2741 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8828
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  11740  Z= 0.106
  Angle     :  0.506   8.119  15940  Z= 0.256
  Chirality :  0.038   0.159   1842
  Planarity :  0.004   0.037   1990
  Dihedral  :  6.389  64.724   1642
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 12.08 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.41 (0.23), residues: 1446
  helix:  2.09 (0.18), residues: 902
  sheet:  None (None), residues: 0
  loop : -1.11 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 278 
 HIS   0.003   0.000   HIS B 515 
 PHE   0.012   0.001   PHE A 101 
 TYR   0.014   0.001   TYR A 781 
 ARG   0.010   0.000   ARG A 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03607 (  655)
  hydrogen bonds       : angle       3.61708 ( 1941)
  SS BOND              : bond        0.00228 (    6)
  SS BOND              : angle       1.36730 (   12)
  covalent geometry    : bond        0.00235 (11734)
  covalent geometry    : angle       0.50525 (15928)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 1.413 
Fit side-chains
REVERT: A  120 CYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7545 (t)
REVERT: A  360 LYS cc_start: 0.8938 (mttt) cc_final: 0.8638 (mtmm)
REVERT: A  401 GLN cc_start: 0.8287 (mt0) cc_final: 0.7993 (mm-40)
REVERT: B  120 CYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7520 (t)
REVERT: B  786 ASP cc_start: 0.8198 (t0) cc_final: 0.7967 (t0)
  outliers start: 11
  outliers final: 4
  residues processed: 108
  average time/residue: 0.1976
  time to fit residues: 34.4493
Evaluate side-chains
  102 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 1.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  120 CYS
Chi-restraints excluded: chain B residue  732 MET
Chi-restraints excluded: chain B residue  761 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 98 optimal weight:    0.3980
   chunk 26 optimal weight:    0.0570
   chunk 72 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
A 515 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.115908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.090479 restraints weight = 13605.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 1.43
r_work: 0.2921 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  11740  Z= 0.102
  Angle     :  0.504   8.069  15940  Z= 0.254
  Chirality :  0.038   0.157   1842
  Planarity :  0.004   0.037   1990
  Dihedral  :  6.300  67.076   1642
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 12.72 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.56 (0.23), residues: 1446
  helix:  2.22 (0.18), residues: 902
  sheet:  None (None), residues: 0
  loop : -1.08 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 278 
 HIS   0.002   0.000   HIS B 515 
 PHE   0.011   0.001   PHE A 429 
 TYR   0.012   0.001   TYR A 781 
 ARG   0.002   0.000   ARG A 861 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03435 (  655)
  hydrogen bonds       : angle       3.56250 ( 1941)
  SS BOND              : bond        0.00057 (    6)
  SS BOND              : angle       1.14945 (   12)
  covalent geometry    : bond        0.00225 (11734)
  covalent geometry    : angle       0.50290 (15928)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 1.220 
Fit side-chains
REVERT: A  120 CYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7429 (t)
REVERT: A  360 LYS cc_start: 0.8923 (mttt) cc_final: 0.8640 (mtmm)
REVERT: A  398 GLU cc_start: 0.8179 (tt0) cc_final: 0.7963 (tt0)
REVERT: A  435 TYR cc_start: 0.8466 (p90) cc_final: 0.7941 (p90)
REVERT: B  120 CYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7548 (t)
  outliers start: 6
  outliers final: 3
  residues processed: 108
  average time/residue: 0.2019
  time to fit residues: 33.7929
Evaluate side-chains
  104 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  120 CYS
Chi-restraints excluded: chain B residue  732 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 83 optimal weight:    6.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    0.2980
   chunk 99 optimal weight:    0.2980
   chunk 43 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 70 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0670
   overall best weight:    1.0720

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

Flipped N/Q/H residues before XYZ refinement:
A 515 HIS
B 455 HIS
B 456 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.114823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.089506 restraints weight = 13658.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 1.42
r_work: 0.2909 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8822
moved from start:          0.1972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  11740  Z= 0.115
  Angle     :  0.513   8.767  15940  Z= 0.259
  Chirality :  0.038   0.155   1842
  Planarity :  0.004   0.038   1990
  Dihedral  :  6.365  66.327   1642
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 12.72 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.58 (0.23), residues: 1446
  helix:  2.23 (0.18), residues: 904
  sheet:  None (None), residues: 0
  loop : -1.07 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 278 
 HIS   0.002   0.001   HIS B 515 
 PHE   0.015   0.001   PHE A 429 
 TYR   0.013   0.001   TYR A 781 
 ARG   0.004   0.000   ARG A 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03603 (  655)
  hydrogen bonds       : angle       3.56793 ( 1941)
  SS BOND              : bond        0.00190 (    6)
  SS BOND              : angle       1.20415 (   12)
  covalent geometry    : bond        0.00268 (11734)
  covalent geometry    : angle       0.51176 (15928)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4692.19 seconds
wall clock time: 82 minutes 25.86 seconds (4945.86 seconds total)