Starting phenix.real_space_refine
on Thu Jul 31 00:04:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b7z_44329/07_2025/9b7z_44329_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b7z_44329/07_2025/9b7z_44329.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b7z_44329/07_2025/9b7z_44329.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b7z_44329/07_2025/9b7z_44329.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b7z_44329/07_2025/9b7z_44329_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b7z_44329/07_2025/9b7z_44329_neut.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      70      5.16       5
     C    8192      2.51       5
     N    2278      2.21       5
     O    2402      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12942
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 854, 6471
          Classifications: {'peptide': 854}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 63, 'TRANS': 790}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 18
  Restraints were copied for chains:
    B
  Time building chain proxies: 15.14, per 1000 atoms: 1.17
  Number of scatterers: 12942
  At special positions: 0
  Unit cell: (102.705, 189.545, 93.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      70     16.00
     O    2402      8.00
     N    2278      7.00
     C    8192      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: 3.64
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3100

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 9 sheets defined
      44.5% alpha, 11.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 29
    Processing helix  chain 'A' and resid 43 through 47
    Processing helix  chain 'A' and resid 68 through 74
      removed outlier: 3.944A  pdb=" N   THR A  74 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 93
    Processing helix  chain 'A' and resid 96 through 101
      removed outlier: 3.714A  pdb=" N   ARG A 101 " --> pdb=" O   ASP A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 120
      removed outlier: 3.949A  pdb=" N   GLU A 118 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 136
      removed outlier: 3.904A  pdb=" N   VAL A 133 " --> pdb=" O   GLY A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 149
      removed outlier: 4.625A  pdb=" N   LEU A 144 " --> pdb=" O   MET A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 161
      No H-bonds generated for 'chain 'A' and resid 159 through 161'
    Processing helix  chain 'A' and resid 162 through 177
    Processing helix  chain 'A' and resid 193 through 203
      removed outlier: 4.379A  pdb=" N   SER A 197 " --> pdb=" O   LYS A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 239
      No H-bonds generated for 'chain 'A' and resid 237 through 239'
    Processing helix  chain 'A' and resid 265 through 281
      removed outlier: 3.713A  pdb=" N   GLN A 269 " --> pdb=" O   SER A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 285
      No H-bonds generated for 'chain 'A' and resid 283 through 285'
    Processing helix  chain 'A' and resid 299 through 312
      removed outlier: 3.862A  pdb=" N   GLN A 303 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 330
    Processing helix  chain 'A' and resid 335 through 351
    Processing helix  chain 'A' and resid 366 through 370
    Processing helix  chain 'A' and resid 415 through 420
      removed outlier: 3.680A  pdb=" N   THR A 419 " --> pdb=" O   PRO A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 444
      removed outlier: 3.582A  pdb=" N   VAL A 434 " --> pdb=" O   THR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 457
    Processing helix  chain 'A' and resid 507 through 512
      removed outlier: 4.000A  pdb=" N   ARG A 512 " --> pdb=" O   SER A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 528
    Processing helix  chain 'A' and resid 533 through 540
      removed outlier: 4.054A  pdb=" N   LEU A 537 " --> pdb=" O   LYS A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 570
      removed outlier: 3.641A  pdb=" N   SER A 552 " --> pdb=" O   ASP A 548 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ILE A 559 " --> pdb=" O   SER A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 592
      removed outlier: 3.819A  pdb=" N   GLY A 588 " --> pdb=" O   GLU A 584 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   TYR A 589 " --> pdb=" O   VAL A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 613
    Processing helix  chain 'A' and resid 626 through 634
      removed outlier: 3.839A  pdb=" N   LYS A 631 " --> pdb=" O   TRP A 627 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLN A 632 " --> pdb=" O   GLU A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 667
      removed outlier: 3.552A  pdb=" N   PHE A 661 " --> pdb=" O   PRO A 657 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL A 662 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   GLU A 663 " --> pdb=" O   PHE A 659 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLN A 664 " --> pdb=" O   GLU A 660 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LYS A 667 " --> pdb=" O   GLU A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 699
      removed outlier: 3.574A  pdb=" N   GLN A 696 " --> pdb=" O   PRO A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 722
    Processing helix  chain 'A' and resid 731 through 740
      removed outlier: 3.524A  pdb=" N   ASN A 735 " --> pdb=" O   SER A 731 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU A 739 " --> pdb=" O   ASN A 735 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL A 740 " --> pdb=" O   VAL A 736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 752
    Processing helix  chain 'A' and resid 767 through 775
      removed outlier: 3.616A  pdb=" N   ARG A 773 " --> pdb=" O   ALA A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 807
      removed outlier: 3.597A  pdb=" N   PHE A 795 " --> pdb=" O   ASP A 791 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY A 807 " --> pdb=" O   LEU A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 815
      removed outlier: 3.501A  pdb=" N   ALA A 814 " --> pdb=" O   ASN A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 834
      removed outlier: 3.792A  pdb=" N   ILE A 834 " --> pdb=" O   SER A 831 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 846 through 850
      removed outlier: 3.708A  pdb=" N   PHE A 850 " --> pdb=" O   ALA A 847 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 29
    Processing helix  chain 'B' and resid 43 through 47
    Processing helix  chain 'B' and resid 68 through 74
      removed outlier: 3.943A  pdb=" N   THR B  74 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 93
    Processing helix  chain 'B' and resid 96 through 101
      removed outlier: 3.713A  pdb=" N   ARG B 101 " --> pdb=" O   ASP B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 120
      removed outlier: 3.950A  pdb=" N   GLU B 118 " --> pdb=" O   SER B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 136
      removed outlier: 3.904A  pdb=" N   VAL B 133 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 149
      removed outlier: 4.626A  pdb=" N   LEU B 144 " --> pdb=" O   MET B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 162 through 177
    Processing helix  chain 'B' and resid 193 through 203
      removed outlier: 4.379A  pdb=" N   SER B 197 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 239
      No H-bonds generated for 'chain 'B' and resid 237 through 239'
    Processing helix  chain 'B' and resid 265 through 281
      removed outlier: 3.713A  pdb=" N   GLN B 269 " --> pdb=" O   SER B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 285
      No H-bonds generated for 'chain 'B' and resid 283 through 285'
    Processing helix  chain 'B' and resid 299 through 312
      removed outlier: 3.862A  pdb=" N   GLN B 303 " --> pdb=" O   VAL B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 330
    Processing helix  chain 'B' and resid 335 through 351
    Processing helix  chain 'B' and resid 366 through 370
    Processing helix  chain 'B' and resid 415 through 420
      removed outlier: 3.680A  pdb=" N   THR B 419 " --> pdb=" O   PRO B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 444
      removed outlier: 3.582A  pdb=" N   VAL B 434 " --> pdb=" O   THR B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 457
    Processing helix  chain 'B' and resid 507 through 512
      removed outlier: 4.000A  pdb=" N   ARG B 512 " --> pdb=" O   SER B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 528
    Processing helix  chain 'B' and resid 533 through 540
      removed outlier: 4.055A  pdb=" N   LEU B 537 " --> pdb=" O   LYS B 533 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 548 through 570
      removed outlier: 3.641A  pdb=" N   SER B 552 " --> pdb=" O   ASP B 548 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ILE B 559 " --> pdb=" O   SER B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 581 through 592
      removed outlier: 3.819A  pdb=" N   GLY B 588 " --> pdb=" O   GLU B 584 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   TYR B 589 " --> pdb=" O   VAL B 585 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 595 through 613
    Processing helix  chain 'B' and resid 626 through 634
      removed outlier: 3.839A  pdb=" N   LYS B 631 " --> pdb=" O   TRP B 627 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLN B 632 " --> pdb=" O   GLU B 628 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 654 through 667
      removed outlier: 3.552A  pdb=" N   PHE B 661 " --> pdb=" O   PRO B 657 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL B 662 " --> pdb=" O   VAL B 658 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   GLU B 663 " --> pdb=" O   PHE B 659 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLN B 664 " --> pdb=" O   GLU B 660 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LYS B 667 " --> pdb=" O   GLU B 663 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 690 through 699
      removed outlier: 3.575A  pdb=" N   GLN B 696 " --> pdb=" O   PRO B 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 718 through 722
    Processing helix  chain 'B' and resid 731 through 740
      removed outlier: 3.523A  pdb=" N   ASN B 735 " --> pdb=" O   SER B 731 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU B 739 " --> pdb=" O   ASN B 735 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL B 740 " --> pdb=" O   VAL B 736 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 748 through 752
    Processing helix  chain 'B' and resid 767 through 775
      removed outlier: 3.616A  pdb=" N   ARG B 773 " --> pdb=" O   ALA B 769 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 791 through 807
      removed outlier: 3.597A  pdb=" N   PHE B 795 " --> pdb=" O   ASP B 791 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY B 807 " --> pdb=" O   LEU B 803 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 811 through 815
      removed outlier: 3.502A  pdb=" N   ALA B 814 " --> pdb=" O   ASN B 811 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 830 through 834
      removed outlier: 3.792A  pdb=" N   ILE B 834 " --> pdb=" O   SER B 831 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 846 through 850
      removed outlier: 3.708A  pdb=" N   PHE B 850 " --> pdb=" O   ALA B 847 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 374 through 376
      removed outlier: 6.048A  pdb=" N   LEU A 320 " --> pdb=" O   GLN A 375 " (cutoff:3.500A)
      removed outlier: 5.429A  pdb=" N   ASN A 387 " --> pdb=" O   PHE A 287 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TYR A 289 " --> pdb=" O   ASN A 387 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ASN A 399 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR A 251 " --> pdb=" O   ASN A 399 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   HIS A 401 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   ALA A 249 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ILE A 403 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ALA A 244 " --> pdb=" O   ILE A   6 " (cutoff:3.500A)
      removed outlier: 4.914A  pdb=" N   VAL A   4 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   LEU A 232 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   MET A   9 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   ALA A 230 " --> pdb=" O   MET A   9 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLY A  11 " --> pdb=" O   VAL A 228 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   VAL A 228 " --> pdb=" O   GLY A  11 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL A 107 " --> pdb=" O   ILE A 155 " (cutoff:3.500A)
      removed outlier: 7.652A  pdb=" N   LEU A 157 " --> pdb=" O   VAL A 107 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ALA A 156 " --> pdb=" O   ASP B 158 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA B 156 " --> pdb=" O   ASP A 158 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL B 107 " --> pdb=" O   ILE B 155 " (cutoff:3.500A)
      removed outlier: 7.652A  pdb=" N   LEU B 157 " --> pdb=" O   VAL B 107 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   VAL B 228 " --> pdb=" O   GLY B  11 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLY B  11 " --> pdb=" O   VAL B 228 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   ALA B 230 " --> pdb=" O   MET B   9 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   MET B   9 " --> pdb=" O   ALA B 230 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   LEU B 232 " --> pdb=" O   ALA B   7 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   VAL B   4 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ALA B 244 " --> pdb=" O   ILE B   6 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ILE B 403 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   ALA B 249 " --> pdb=" O   HIS B 401 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   HIS B 401 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR B 251 " --> pdb=" O   ASN B 399 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ASN B 399 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 5.428A  pdb=" N   ASN B 387 " --> pdb=" O   PHE B 287 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 387 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   LEU B 320 " --> pdb=" O   GLN B 375 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 353
      removed outlier: 3.892A  pdb=" N   LEU A 381 " --> pdb=" O   TRP A 353 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 422 through 428
    Processing sheet with id=AA4, first strand: chain 'A' and resid 712 through 713
      removed outlier: 6.674A  pdb=" N   ILE A 577 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   CYS A 496 " --> pdb=" O   VAL A 578 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   TRP A 493 " --> pdb=" O   LEU A 759 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ILE A 761 " --> pdb=" O   TRP A 493 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ILE A 495 " --> pdb=" O   ILE A 761 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 622 through 623
      removed outlier: 6.383A  pdb=" N   THR A 650 " --> pdb=" O   ALA A 641 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL A 639 " --> pdb=" O   SER A 652 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 352 through 353
      removed outlier: 3.892A  pdb=" N   LEU B 381 " --> pdb=" O   TRP B 353 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 422 through 428
    Processing sheet with id=AA8, first strand: chain 'B' and resid 712 through 713
      removed outlier: 6.674A  pdb=" N   ILE B 577 " --> pdb=" O   LEU B 713 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   CYS B 496 " --> pdb=" O   VAL B 578 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   TRP B 493 " --> pdb=" O   LEU B 759 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ILE B 761 " --> pdb=" O   TRP B 493 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ILE B 495 " --> pdb=" O   ILE B 761 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 622 through 623
      removed outlier: 6.382A  pdb=" N   THR B 650 " --> pdb=" O   ALA B 641 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL B 639 " --> pdb=" O   SER B 652 " (cutoff:3.500A)

    532 hydrogen bonds defined for protein.
    1452 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: 4.68

  Time building geometry restraints manager: 4.29 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: 4042
        1.34 -     1.46: 2159
        1.46 -     1.57: 6943
        1.57 -     1.69: 2
        1.69 -     1.81: 110
  Bond restraints: 13256
  Sorted by residual:
  bond pdb=" N   LEU A 615 "
       pdb=" CA  LEU A 615 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 8.30e-03 1.45e+04 1.78e+01
  bond pdb=" N   LEU B 615 "
       pdb=" CA  LEU B 615 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 8.30e-03 1.45e+04 1.67e+01
  bond pdb=" N   GLY B 618 "
       pdb=" CA  GLY B 618 "
    ideal  model  delta    sigma   weight residual
    1.443  1.476 -0.033 8.60e-03 1.35e+04 1.47e+01
  bond pdb=" N   GLY A 618 "
       pdb=" CA  GLY A 618 "
    ideal  model  delta    sigma   weight residual
    1.443  1.476 -0.033 8.60e-03 1.35e+04 1.44e+01
  bond pdb=" N   VAL B 111 "
       pdb=" CA  VAL B 111 "
    ideal  model  delta    sigma   weight residual
    1.455  1.492 -0.037 1.18e-02 7.18e+03 9.90e+00
  ... (remaining 13251 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 17535
        2.68 -     5.37: 433
        5.37 -     8.05: 48
        8.05 -    10.74: 10
       10.74 -    13.42: 4
  Bond angle restraints: 18030
  Sorted by residual:
  angle pdb=" N   GLU A 668 "
        pdb=" CA  GLU A 668 "
        pdb=" C   GLU A 668 "
      ideal   model   delta    sigma   weight residual
     108.00  115.53   -7.53 1.48e+00 4.57e-01 2.59e+01
  angle pdb=" N   GLU B 668 "
        pdb=" CA  GLU B 668 "
        pdb=" C   GLU B 668 "
      ideal   model   delta    sigma   weight residual
     108.00  115.52   -7.52 1.48e+00 4.57e-01 2.58e+01
  angle pdb=" CA  GLU A 489 "
        pdb=" CB  GLU A 489 "
        pdb=" CG  GLU A 489 "
      ideal   model   delta    sigma   weight residual
     114.10  123.56   -9.46 2.00e+00 2.50e-01 2.24e+01
  angle pdb=" CA  GLU B 489 "
        pdb=" CB  GLU B 489 "
        pdb=" CG  GLU B 489 "
      ideal   model   delta    sigma   weight residual
     114.10  123.52   -9.42 2.00e+00 2.50e-01 2.22e+01
  angle pdb=" CB  MET A 570 "
        pdb=" CG  MET A 570 "
        pdb=" SD  MET A 570 "
      ideal   model   delta    sigma   weight residual
     112.70  126.12  -13.42 3.00e+00 1.11e-01 2.00e+01
  ... (remaining 18025 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.18: 7148
       18.18 -    36.37: 612
       36.37 -    54.55: 160
       54.55 -    72.73: 38
       72.73 -    90.92: 10
  Dihedral angle restraints: 7968
    sinusoidal: 3138
      harmonic: 4830
  Sorted by residual:
  dihedral pdb=" CA  GLU A 820 "
           pdb=" C   GLU A 820 "
           pdb=" N   PHE A 821 "
           pdb=" CA  PHE A 821 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.99  -21.01     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  GLU B 820 "
           pdb=" C   GLU B 820 "
           pdb=" N   PHE B 821 "
           pdb=" CA  PHE B 821 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.04  -20.96     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  ASP A 547 "
           pdb=" C   ASP A 547 "
           pdb=" N   ASP A 548 "
           pdb=" CA  ASP A 548 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.08   16.92     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 7965 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1274
       0.049 -    0.097: 497
       0.097 -    0.146: 190
       0.146 -    0.195: 30
       0.195 -    0.243: 11
  Chirality restraints: 2002
  Sorted by residual:
  chirality pdb=" CA  GLU B 668 "
            pdb=" N   GLU B 668 "
            pdb=" C   GLU B 668 "
            pdb=" CB  GLU B 668 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  GLU A 668 "
            pdb=" N   GLU A 668 "
            pdb=" C   GLU A 668 "
            pdb=" CB  GLU A 668 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  PHE A 821 "
            pdb=" N   PHE A 821 "
            pdb=" C   PHE A 821 "
            pdb=" CB  PHE A 821 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 1999 not shown)

  Planarity restraints: 2382
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 737 "    0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" CG  ASN B 737 "   -0.055 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 737 "    0.021 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 737 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 737 "   -0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" CG  ASN A 737 "    0.055 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 737 "   -0.021 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 737 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 460 "   -0.043 5.00e-02 4.00e+02   6.55e-02 6.85e+00
        pdb=" N   PRO A 461 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 461 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 461 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 2379 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 3195
        2.80 -     3.32: 10983
        3.32 -     3.85: 21462
        3.85 -     4.37: 25548
        4.37 -     4.90: 43893
  Nonbonded interactions: 105081
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 253 "
            pdb=" O   GLY B 152 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   GLY A 152 "
            pdb=" OG1 THR B 253 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   LEU B  13 "
            pdb=" OG  SER B  16 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" O   LEU A  13 "
            pdb=" OG  SER A  16 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" O   LEU B  82 "
            pdb=" OG1 THR B  86 "
     model   vdw
     2.324 3.040
  ... (remaining 105076 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.100
  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:             0.020
  Extract box with map and model:          0.640
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     40.850
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9073
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.061  13256  Z= 0.400
  Angle     :  1.000  13.425  18030  Z= 0.593
  Chirality :  0.060   0.243   2002
  Planarity :  0.009   0.093   2382
  Dihedral  : 15.376  90.917   4868
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 17.22 %
    Favored  : 82.49 %
  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: -1.72 (0.18), residues: 1704
  helix: -1.60 (0.17), residues: 582
  sheet:  0.36 (0.36), residues: 206
  loop : -1.12 (0.18), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 750 
 HIS   0.011   0.002   HIS A  68 
 PHE   0.015   0.002   PHE B 546 
 TYR   0.022   0.003   TYR B 130 
 ARG   0.021   0.001   ARG A 773 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23567 (  532)
  hydrogen bonds       : angle       7.47465 ( 1452)
  covalent geometry    : bond        0.00754 (13256)
  covalent geometry    : angle       1.00049 (18030)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 157
  time to evaluate  : 1.430 
Fit side-chains
REVERT: A  240 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.8361 (mmp-170)
REVERT: A  495 ILE cc_start: 0.9244 (mt) cc_final: 0.8753 (mp)
REVERT: A  556 LEU cc_start: 0.9301 (mm) cc_final: 0.9031 (mp)
REVERT: A  611 LYS cc_start: 0.9109 (tttt) cc_final: 0.8830 (ptmt)
REVERT: A  627 TRP cc_start: 0.8415 (t-100) cc_final: 0.8114 (t-100)
REVERT: A  680 MET cc_start: 0.8924 (tpp) cc_final: 0.8451 (tpt)
REVERT: A  682 PHE cc_start: 0.8966 (m-80) cc_final: 0.8556 (m-80)
REVERT: B  240 ARG cc_start: 0.8590 (mmt-90) cc_final: 0.8372 (mmp-170)
REVERT: B  495 ILE cc_start: 0.9230 (mt) cc_final: 0.8727 (mp)
REVERT: B  556 LEU cc_start: 0.9307 (mm) cc_final: 0.9043 (mp)
REVERT: B  611 LYS cc_start: 0.9116 (tttt) cc_final: 0.8834 (ptmt)
REVERT: B  627 TRP cc_start: 0.8380 (t-100) cc_final: 0.8126 (t-100)
REVERT: B  680 MET cc_start: 0.8912 (tpp) cc_final: 0.8422 (tpt)
REVERT: B  682 PHE cc_start: 0.8990 (m-80) cc_final: 0.8573 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 161
  average time/residue: 1.6399
  time to fit residues: 284.1990
Evaluate side-chains
  106 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 1.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 GLU
Chi-restraints excluded: chain B residue  704 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 143 optimal weight:    8.9990
   chunk 128 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   chunk 133 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9990
   chunk 154 optimal weight:    0.6980
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 551 HIS
A 655 GLN
A 737 ASN
B 551 HIS
B 655 GLN
B 737 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.086917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.049928 restraints weight = 28770.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.2705 rms_B_bonded: 2.63
r_work: 0.2588 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2470 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9045
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13256  Z= 0.149
  Angle     :  0.624   7.821  18030  Z= 0.316
  Chirality :  0.044   0.148   2002
  Planarity :  0.006   0.053   2382
  Dihedral  :  6.444 137.339   1826
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.44 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.41 (0.19), residues: 1704
  helix: -0.05 (0.20), residues: 608
  sheet:  0.53 (0.34), residues: 216
  loop : -0.55 (0.20), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  40 
 HIS   0.005   0.001   HIS B  68 
 PHE   0.016   0.001   PHE A 530 
 TYR   0.023   0.002   TYR B 277 
 ARG   0.006   0.000   ARG A 790 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05387 (  532)
  hydrogen bonds       : angle       5.22510 ( 1452)
  covalent geometry    : bond        0.00346 (13256)
  covalent geometry    : angle       0.62416 (18030)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 105
  time to evaluate  : 1.405 
Fit side-chains
REVERT: A  240 ARG cc_start: 0.9080 (mmt-90) cc_final: 0.8213 (mmm160)
REVERT: A  530 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7855 (t80)
REVERT: A  556 LEU cc_start: 0.9186 (mm) cc_final: 0.8962 (mp)
REVERT: A  611 LYS cc_start: 0.9100 (tttt) cc_final: 0.8895 (ptmt)
REVERT: A  680 MET cc_start: 0.9003 (tpp) cc_final: 0.8670 (mpp)
REVERT: A  682 PHE cc_start: 0.8653 (m-80) cc_final: 0.8357 (m-80)
REVERT: B  240 ARG cc_start: 0.9079 (mmt-90) cc_final: 0.8220 (mmm160)
REVERT: B  499 MET cc_start: 0.8834 (pmm) cc_final: 0.8547 (pmm)
REVERT: B  556 LEU cc_start: 0.9197 (mm) cc_final: 0.8972 (mp)
REVERT: B  611 LYS cc_start: 0.9089 (tttt) cc_final: 0.8872 (ptmt)
REVERT: B  680 MET cc_start: 0.8999 (tpp) cc_final: 0.8673 (mpp)
REVERT: B  682 PHE cc_start: 0.8684 (m-80) cc_final: 0.8469 (m-80)
REVERT: B  687 MET cc_start: 0.8297 (mtm) cc_final: 0.8078 (mtt)
  outliers start: 34
  outliers final: 14
  residues processed: 130
  average time/residue: 1.3710
  time to fit residues: 194.1413
Evaluate side-chains
  107 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 1.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  704 GLU
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  704 GLU
Chi-restraints excluded: chain B residue  743 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9990
   chunk 85 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 139 optimal weight:   20.0000
   chunk 51 optimal weight:    5.9990
   chunk 118 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 135 optimal weight:    5.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 737 ASN
B 737 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.085296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.048094 restraints weight = 29047.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.2662 rms_B_bonded: 2.65
r_work: 0.2541 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2425 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9085
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  13256  Z= 0.172
  Angle     :  0.615   8.268  18030  Z= 0.306
  Chirality :  0.045   0.166   2002
  Planarity :  0.005   0.049   2382
  Dihedral  :  4.792  55.434   1826
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.28 %
    Favored  : 80.82 %
  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:  0.14 (0.20), residues: 1704
  helix:  0.52 (0.21), residues: 612
  sheet:  0.55 (0.34), residues: 226
  loop : -0.24 (0.21), residues: 866

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 627 
 HIS   0.004   0.001   HIS A  68 
 PHE   0.012   0.001   PHE A 530 
 TYR   0.022   0.002   TYR B 277 
 ARG   0.004   0.000   ARG A 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05258 (  532)
  hydrogen bonds       : angle       5.02011 ( 1452)
  covalent geometry    : bond        0.00411 (13256)
  covalent geometry    : angle       0.61536 (18030)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 102
  time to evaluate  : 1.425 
Fit side-chains
REVERT: A  240 ARG cc_start: 0.9097 (mmt-90) cc_final: 0.8281 (mmm160)
REVERT: A  530 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7827 (t80)
REVERT: A  556 LEU cc_start: 0.9184 (mm) cc_final: 0.8943 (mp)
REVERT: A  573 ARG cc_start: 0.8751 (mmm-85) cc_final: 0.8355 (mmm160)
REVERT: A  611 LYS cc_start: 0.9100 (tttt) cc_final: 0.8855 (ptmt)
REVERT: A  680 MET cc_start: 0.9059 (tpp) cc_final: 0.8541 (mpp)
REVERT: A  721 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8865 (mp10)
REVERT: A  825 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8460 (ptt90)
REVERT: B  240 ARG cc_start: 0.9095 (mmt-90) cc_final: 0.8295 (mmm160)
REVERT: B  499 MET cc_start: 0.8819 (pmm) cc_final: 0.8584 (pmm)
REVERT: B  556 LEU cc_start: 0.9182 (mm) cc_final: 0.8954 (mp)
REVERT: B  573 ARG cc_start: 0.8710 (mmm-85) cc_final: 0.8312 (mmm160)
REVERT: B  680 MET cc_start: 0.9108 (tpp) cc_final: 0.8657 (mpp)
REVERT: B  682 PHE cc_start: 0.8628 (m-80) cc_final: 0.8310 (m-80)
REVERT: B  687 MET cc_start: 0.8296 (mtm) cc_final: 0.8041 (mtt)
REVERT: B  721 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8879 (mp10)
REVERT: B  825 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8474 (ptt90)
  outliers start: 40
  outliers final: 18
  residues processed: 132
  average time/residue: 1.5022
  time to fit residues: 214.9820
Evaluate side-chains
  113 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 1.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  704 GLU
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  825 ARG
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  702 ILE
Chi-restraints excluded: chain B residue  704 GLU
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Chi-restraints excluded: chain B residue  825 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 150 optimal weight:    9.9990
   chunk 72 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 162 optimal weight:    4.9990
   chunk 114 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 89 optimal weight:    0.6980
   chunk 140 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    1.6584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.084767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.047808 restraints weight = 28733.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.2640 rms_B_bonded: 2.64
r_work: 0.2515 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2397 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9091
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13256  Z= 0.173
  Angle     :  0.607   8.165  18030  Z= 0.300
  Chirality :  0.045   0.177   2002
  Planarity :  0.005   0.047   2382
  Dihedral  :  5.916 121.627   1826
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 16.79 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.41 (0.20), residues: 1704
  helix:  0.81 (0.21), residues: 610
  sheet:  0.62 (0.34), residues: 226
  loop : -0.11 (0.21), residues: 868

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  40 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.017   0.001   PHE A 682 
 TYR   0.021   0.002   TYR A 277 
 ARG   0.005   0.000   ARG A 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05016 (  532)
  hydrogen bonds       : angle       4.90528 ( 1452)
  covalent geometry    : bond        0.00417 (13256)
  covalent geometry    : angle       0.60682 (18030)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 94
  time to evaluate  : 1.509 
Fit side-chains
REVERT: A   57 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9425 (mp)
REVERT: A  240 ARG cc_start: 0.9081 (mmt-90) cc_final: 0.7976 (mmm160)
REVERT: A  465 MET cc_start: 0.9547 (OUTLIER) cc_final: 0.8822 (mtm)
REVERT: A  499 MET cc_start: 0.8812 (pmm) cc_final: 0.7998 (ptt)
REVERT: A  530 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7804 (t80)
REVERT: A  573 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.8316 (mmm160)
REVERT: A  680 MET cc_start: 0.9112 (tpp) cc_final: 0.8451 (mpp)
REVERT: A  682 PHE cc_start: 0.8560 (m-80) cc_final: 0.8222 (m-80)
REVERT: A  721 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8856 (mp10)
REVERT: B   57 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9425 (mp)
REVERT: B  240 ARG cc_start: 0.9075 (mmt-90) cc_final: 0.8032 (mmm160)
REVERT: B  499 MET cc_start: 0.8839 (pmm) cc_final: 0.8603 (pmm)
REVERT: B  556 LEU cc_start: 0.9157 (mm) cc_final: 0.8954 (mp)
REVERT: B  573 ARG cc_start: 0.8713 (mmm-85) cc_final: 0.8281 (mmm160)
REVERT: B  680 MET cc_start: 0.9103 (tpp) cc_final: 0.8608 (mpp)
REVERT: B  682 PHE cc_start: 0.8591 (m-80) cc_final: 0.8366 (m-80)
REVERT: B  721 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8857 (mp10)
  outliers start: 43
  outliers final: 21
  residues processed: 124
  average time/residue: 1.3562
  time to fit residues: 183.4693
Evaluate side-chains
  119 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 1.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  407 ASN
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  407 ASN
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  702 ILE
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 45 optimal weight:    0.7980
   chunk 153 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 152 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 162 optimal weight:    7.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 789 HIS
B 789 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.084396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.047401 restraints weight = 29108.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.2638 rms_B_bonded: 2.63
r_work: 0.2517 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2401 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9098
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13256  Z= 0.180
  Angle     :  0.618   9.842  18030  Z= 0.305
  Chirality :  0.045   0.169   2002
  Planarity :  0.005   0.046   2382
  Dihedral  :  4.105  18.057   1820
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.44 %
    Favored  : 79.59 %
  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:  0.54 (0.20), residues: 1704
  helix:  1.00 (0.21), residues: 610
  sheet:  0.56 (0.33), residues: 246
  loop : -0.08 (0.22), residues: 848

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  40 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.013   0.001   PHE A 682 
 TYR   0.021   0.002   TYR B 277 
 ARG   0.010   0.000   ARG B 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05033 (  532)
  hydrogen bonds       : angle       4.86486 ( 1452)
  covalent geometry    : bond        0.00434 (13256)
  covalent geometry    : angle       0.61848 (18030)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 94
  time to evaluate  : 1.483 
Fit side-chains
REVERT: A   57 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9425 (mp)
REVERT: A  240 ARG cc_start: 0.9079 (mmt-90) cc_final: 0.8031 (mmm160)
REVERT: A  499 MET cc_start: 0.8767 (pmm) cc_final: 0.8044 (ptt)
REVERT: A  530 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7779 (t80)
REVERT: A  573 ARG cc_start: 0.8770 (mmm-85) cc_final: 0.8318 (mmm160)
REVERT: A  680 MET cc_start: 0.9105 (tpp) cc_final: 0.8444 (mpp)
REVERT: A  682 PHE cc_start: 0.8514 (m-80) cc_final: 0.8123 (m-80)
REVERT: A  687 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8063 (ptp)
REVERT: A  721 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8861 (mp10)
REVERT: B   57 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9424 (mp)
REVERT: B  240 ARG cc_start: 0.9095 (mmt-90) cc_final: 0.7988 (mmm160)
REVERT: B  465 MET cc_start: 0.9541 (OUTLIER) cc_final: 0.8792 (mtm)
REVERT: B  573 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8271 (mmm160)
REVERT: B  680 MET cc_start: 0.9020 (tpp) cc_final: 0.8539 (mpp)
REVERT: B  682 PHE cc_start: 0.8622 (m-80) cc_final: 0.8374 (m-80)
REVERT: B  721 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8801 (mp10)
  outliers start: 41
  outliers final: 24
  residues processed: 122
  average time/residue: 1.5021
  time to fit residues: 198.8295
Evaluate side-chains
  116 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 85
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  407 ASN
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  687 MET
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  407 ASN
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  702 ILE
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 135 optimal weight:    5.9990
   chunk 161 optimal weight:    0.9990
   chunk 110 optimal weight:    5.9990
   chunk 96 optimal weight:    0.1980
   chunk 36 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 136 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 331 HIS
B 331 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.084470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.047458 restraints weight = 29431.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.2644 rms_B_bonded: 2.66
r_work: 0.2523 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2407 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9098
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13256  Z= 0.168
  Angle     :  0.608   8.523  18030  Z= 0.297
  Chirality :  0.045   0.162   2002
  Planarity :  0.004   0.045   2382
  Dihedral  :  4.051  17.714   1820
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 17.44 %
    Favored  : 79.45 %
  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:  0.58 (0.21), residues: 1704
  helix:  1.01 (0.21), residues: 624
  sheet:  0.47 (0.32), residues: 256
  loop : -0.02 (0.23), residues: 824

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  40 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.011   0.001   PHE A 682 
 TYR   0.021   0.002   TYR A 277 
 ARG   0.005   0.000   ARG B 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04843 (  532)
  hydrogen bonds       : angle       4.82420 ( 1452)
  covalent geometry    : bond        0.00403 (13256)
  covalent geometry    : angle       0.60811 (18030)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 92
  time to evaluate  : 1.400 
Fit side-chains
REVERT: A   57 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9438 (mp)
REVERT: A  240 ARG cc_start: 0.9071 (mmt-90) cc_final: 0.8020 (mmm160)
REVERT: A  499 MET cc_start: 0.8729 (pmm) cc_final: 0.8039 (ptt)
REVERT: A  530 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7810 (t80)
REVERT: A  573 ARG cc_start: 0.8781 (mmm-85) cc_final: 0.8355 (mmm160)
REVERT: A  680 MET cc_start: 0.9071 (tpp) cc_final: 0.8447 (mpp)
REVERT: A  682 PHE cc_start: 0.8440 (m-80) cc_final: 0.8009 (m-80)
REVERT: A  687 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8091 (ptp)
REVERT: A  721 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8812 (mp10)
REVERT: B   57 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9439 (mp)
REVERT: B  240 ARG cc_start: 0.9072 (mmt-90) cc_final: 0.8007 (mmm160)
REVERT: B  465 MET cc_start: 0.9540 (OUTLIER) cc_final: 0.8782 (mtm)
REVERT: B  499 MET cc_start: 0.8705 (pmm) cc_final: 0.7991 (ptt)
REVERT: B  573 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.8286 (mmm160)
REVERT: B  680 MET cc_start: 0.8933 (tpp) cc_final: 0.8473 (mpp)
REVERT: B  682 PHE cc_start: 0.8588 (m-80) cc_final: 0.8232 (m-80)
REVERT: B  687 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8385 (ptp)
REVERT: B  721 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8808 (mp10)
  outliers start: 43
  outliers final: 23
  residues processed: 121
  average time/residue: 1.2029
  time to fit residues: 159.9231
Evaluate side-chains
  115 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 84
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  407 ASN
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  687 MET
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  407 ASN
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  687 MET
Chi-restraints excluded: chain B residue  702 ILE
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 164 optimal weight:    0.6980
   chunk 153 optimal weight:   10.0000
   chunk 3 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9990
   chunk 150 optimal weight:    7.9990
   chunk 34 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 156 optimal weight:   10.0000
   overall best weight:    1.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.084839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.047795 restraints weight = 28955.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.2653 rms_B_bonded: 2.65
r_work: 0.2532 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2414 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9087
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13256  Z= 0.141
  Angle     :  0.589   8.700  18030  Z= 0.288
  Chirality :  0.044   0.166   2002
  Planarity :  0.004   0.045   2382
  Dihedral  :  3.962  17.026   1820
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.93 %
    Favored  : 79.81 %
  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:  0.67 (0.21), residues: 1704
  helix:  1.12 (0.21), residues: 624
  sheet:  0.51 (0.32), residues: 256
  loop :  0.01 (0.23), residues: 824

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  40 
 HIS   0.003   0.001   HIS A  68 
 PHE   0.011   0.001   PHE A 682 
 TYR   0.021   0.002   TYR B 277 
 ARG   0.012   0.000   ARG A 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04537 (  532)
  hydrogen bonds       : angle       4.75200 ( 1452)
  covalent geometry    : bond        0.00339 (13256)
  covalent geometry    : angle       0.58880 (18030)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 93
  time to evaluate  : 1.384 
Fit side-chains
REVERT: A   57 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9450 (mp)
REVERT: A  240 ARG cc_start: 0.9062 (mmt-90) cc_final: 0.7967 (mmm160)
REVERT: A  465 MET cc_start: 0.9530 (OUTLIER) cc_final: 0.8750 (mtm)
REVERT: A  499 MET cc_start: 0.8724 (pmm) cc_final: 0.8060 (ptt)
REVERT: A  530 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7847 (t80)
REVERT: A  573 ARG cc_start: 0.8798 (mmm-85) cc_final: 0.8376 (mmm160)
REVERT: A  680 MET cc_start: 0.9078 (tpp) cc_final: 0.8487 (mpp)
REVERT: A  682 PHE cc_start: 0.8390 (m-80) cc_final: 0.7955 (m-80)
REVERT: A  687 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8229 (ptp)
REVERT: A  721 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8810 (mp10)
REVERT: B   57 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9450 (mp)
REVERT: B  240 ARG cc_start: 0.9064 (mmt-90) cc_final: 0.7979 (mmm160)
REVERT: B  499 MET cc_start: 0.8719 (pmm) cc_final: 0.8004 (ptt)
REVERT: B  573 ARG cc_start: 0.8769 (mmm-85) cc_final: 0.8340 (mmm160)
REVERT: B  680 MET cc_start: 0.8956 (tpp) cc_final: 0.8522 (mpp)
REVERT: B  682 PHE cc_start: 0.8563 (m-80) cc_final: 0.8203 (m-80)
REVERT: B  687 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8397 (ptp)
REVERT: B  721 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8822 (mp10)
  outliers start: 45
  outliers final: 19
  residues processed: 126
  average time/residue: 1.2224
  time to fit residues: 169.4072
Evaluate side-chains
  111 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 84
  time to evaluate  : 1.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  687 MET
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  704 GLU
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  687 MET
Chi-restraints excluded: chain B residue  704 GLU
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 48 optimal weight:    0.2980
   chunk 67 optimal weight:    6.9990
   chunk 105 optimal weight:    0.0270
   chunk 161 optimal weight:    4.9990
   chunk 138 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0040
   chunk 119 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.4250

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

Flipped N/Q/H residues before XYZ refinement:
A 328 ASN
** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.086411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.049849 restraints weight = 28990.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.2714 rms_B_bonded: 2.67
r_work: 0.2597 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2482 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9053
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  13256  Z= 0.100
  Angle     :  0.580   9.940  18030  Z= 0.280
  Chirality :  0.043   0.173   2002
  Planarity :  0.004   0.045   2382
  Dihedral  :  3.759  16.577   1820
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 18.31 %
    Favored  : 79.81 %
  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:  0.89 (0.21), residues: 1704
  helix:  1.48 (0.22), residues: 610
  sheet:  0.45 (0.32), residues: 258
  loop :  0.06 (0.22), residues: 836

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  40 
 HIS   0.002   0.000   HIS B  68 
 PHE   0.010   0.001   PHE A 682 
 TYR   0.021   0.001   TYR B 277 
 ARG   0.011   0.000   ARG B 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03688 (  532)
  hydrogen bonds       : angle       4.59618 ( 1452)
  covalent geometry    : bond        0.00225 (13256)
  covalent geometry    : angle       0.57976 (18030)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 1.325 
Fit side-chains
   revert: symmetry clash
REVERT: A  240 ARG cc_start: 0.9030 (mmt-90) cc_final: 0.8004 (mmm160)
REVERT: A  465 MET cc_start: 0.9499 (OUTLIER) cc_final: 0.8708 (mtm)
REVERT: A  499 MET cc_start: 0.8678 (pmm) cc_final: 0.7996 (ptt)
REVERT: A  530 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7872 (t80)
REVERT: A  573 ARG cc_start: 0.8840 (mmm-85) cc_final: 0.8421 (mmm160)
REVERT: A  680 MET cc_start: 0.9056 (tpp) cc_final: 0.8522 (mpp)
REVERT: A  682 PHE cc_start: 0.8402 (m-80) cc_final: 0.8006 (m-80)
REVERT: A  687 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8115 (ptp)
REVERT: A  721 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8803 (mp10)
REVERT: B  240 ARG cc_start: 0.9030 (mmt-90) cc_final: 0.8013 (mmm160)
REVERT: B  465 MET cc_start: 0.9505 (OUTLIER) cc_final: 0.8746 (mtm)
REVERT: B  499 MET cc_start: 0.8705 (pmm) cc_final: 0.7994 (ptt)
REVERT: B  530 PHE cc_start: 0.8154 (t80) cc_final: 0.7709 (t80)
REVERT: B  573 ARG cc_start: 0.8824 (mmm-85) cc_final: 0.8405 (mmm160)
REVERT: B  680 MET cc_start: 0.8945 (tpp) cc_final: 0.8548 (mpp)
REVERT: B  682 PHE cc_start: 0.8499 (m-80) cc_final: 0.8126 (m-80)
REVERT: B  687 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8329 (ptp)
REVERT: B  721 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8793 (mp10)
  outliers start: 26
  outliers final: 13
  residues processed: 114
  average time/residue: 1.1579
  time to fit residues: 145.8725
Evaluate side-chains
  107 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 1.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  687 MET
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  687 MET
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 136 optimal weight:    3.9990
   chunk 11 optimal weight:    0.3980
   chunk 148 optimal weight:    0.4980
   chunk 169 optimal weight:    1.9990
   chunk 110 optimal weight:    0.0770
   chunk 29 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 113 optimal weight:    0.3980
   chunk 106 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.6740

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

Flipped N/Q/H residues before XYZ refinement:
B 746 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.086000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.049127 restraints weight = 28738.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.2700 rms_B_bonded: 2.65
r_work: 0.2584 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2473 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9081
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13256  Z= 0.108
  Angle     :  0.592  11.484  18030  Z= 0.287
  Chirality :  0.043   0.171   2002
  Planarity :  0.004   0.046   2382
  Dihedral  :  3.695  16.204   1820
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.23 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.95 (0.21), residues: 1704
  helix:  1.52 (0.22), residues: 616
  sheet:  0.36 (0.32), residues: 260
  loop :  0.15 (0.23), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  40 
 HIS   0.002   0.000   HIS B  68 
 PHE   0.010   0.001   PHE A 682 
 TYR   0.021   0.002   TYR B 277 
 ARG   0.010   0.000   ARG A 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03851 (  532)
  hydrogen bonds       : angle       4.54363 ( 1452)
  covalent geometry    : bond        0.00252 (13256)
  covalent geometry    : angle       0.59202 (18030)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 93
  time to evaluate  : 1.578 
Fit side-chains
REVERT: A   57 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9460 (mp)
REVERT: A  240 ARG cc_start: 0.9018 (mmt-90) cc_final: 0.8060 (mmm160)
REVERT: A  465 MET cc_start: 0.9497 (OUTLIER) cc_final: 0.8686 (mtm)
REVERT: A  499 MET cc_start: 0.8693 (pmm) cc_final: 0.8028 (ptt)
REVERT: A  530 PHE cc_start: 0.8428 (t80) cc_final: 0.7975 (t80)
REVERT: A  573 ARG cc_start: 0.8844 (mmm-85) cc_final: 0.8420 (mmm160)
REVERT: A  680 MET cc_start: 0.9059 (tpp) cc_final: 0.8484 (mpp)
REVERT: A  682 PHE cc_start: 0.8461 (m-80) cc_final: 0.8045 (m-80)
REVERT: A  687 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8177 (ptp)
REVERT: A  721 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8804 (mp10)
REVERT: B   57 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9458 (mp)
REVERT: B  240 ARG cc_start: 0.9021 (mmt-90) cc_final: 0.8058 (mmm160)
REVERT: B  465 MET cc_start: 0.9514 (OUTLIER) cc_final: 0.8742 (mtm)
REVERT: B  499 MET cc_start: 0.8725 (pmm) cc_final: 0.8026 (ptt)
REVERT: B  530 PHE cc_start: 0.8213 (t80) cc_final: 0.7726 (t80)
REVERT: B  573 ARG cc_start: 0.8837 (mmm-85) cc_final: 0.8413 (mmm160)
REVERT: B  680 MET cc_start: 0.8942 (tpp) cc_final: 0.8544 (mpp)
REVERT: B  682 PHE cc_start: 0.8515 (m-80) cc_final: 0.8146 (m-80)
REVERT: B  687 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8368 (ptp)
REVERT: B  721 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8800 (mp10)
  outliers start: 31
  outliers final: 16
  residues processed: 116
  average time/residue: 1.1682
  time to fit residues: 149.8503
Evaluate side-chains
  111 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 1.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  687 MET
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  687 MET
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 131 optimal weight:    0.9980
   chunk 86 optimal weight:    0.4980
   chunk 62 optimal weight:   10.0000
   chunk 59 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 163 optimal weight:    3.9990
   chunk 70 optimal weight:   20.0000
   chunk 46 optimal weight:    1.9990
   chunk 160 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0000
   overall best weight:    0.5184

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.086682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.050085 restraints weight = 28959.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.2695 rms_B_bonded: 2.67
r_work: 0.2574 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2456 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9047
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  13256  Z= 0.101
  Angle     :  0.596  11.657  18030  Z= 0.287
  Chirality :  0.043   0.172   2002
  Planarity :  0.004   0.046   2382
  Dihedral  :  3.615  15.653   1820
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.74 %
    Favored  : 79.31 %
  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:  1.04 (0.21), residues: 1704
  helix:  1.63 (0.22), residues: 616
  sheet:  0.36 (0.32), residues: 260
  loop :  0.20 (0.23), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  40 
 HIS   0.002   0.000   HIS B 580 
 PHE   0.010   0.001   PHE A 682 
 TYR   0.020   0.001   TYR B 277 
 ARG   0.014   0.000   ARG A 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03568 (  532)
  hydrogen bonds       : angle       4.49438 ( 1452)
  covalent geometry    : bond        0.00236 (13256)
  covalent geometry    : angle       0.59565 (18030)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 89
  time to evaluate  : 1.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 ARG cc_start: 0.9041 (mmt-90) cc_final: 0.8045 (mmm160)
REVERT: A  465 MET cc_start: 0.9466 (OUTLIER) cc_final: 0.8649 (mtm)
REVERT: A  499 MET cc_start: 0.8655 (pmm) cc_final: 0.8044 (ptt)
REVERT: A  530 PHE cc_start: 0.8369 (t80) cc_final: 0.7999 (t80)
REVERT: A  573 ARG cc_start: 0.8891 (mmm-85) cc_final: 0.8462 (mmm160)
REVERT: A  680 MET cc_start: 0.9044 (tpp) cc_final: 0.8548 (mpp)
REVERT: A  682 PHE cc_start: 0.8387 (m-80) cc_final: 0.8119 (m-80)
REVERT: A  687 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8165 (ptp)
REVERT: A  721 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8832 (mp10)
REVERT: B  240 ARG cc_start: 0.9042 (mmt-90) cc_final: 0.8041 (mmm160)
REVERT: B  465 MET cc_start: 0.9481 (OUTLIER) cc_final: 0.8699 (mtm)
REVERT: B  499 MET cc_start: 0.8723 (pmm) cc_final: 0.8022 (ptt)
REVERT: B  530 PHE cc_start: 0.8223 (t80) cc_final: 0.7742 (t80)
REVERT: B  573 ARG cc_start: 0.8883 (mmm-85) cc_final: 0.8460 (mmm160)
REVERT: B  680 MET cc_start: 0.8958 (tpp) cc_final: 0.8599 (mpp)
REVERT: B  682 PHE cc_start: 0.8422 (m-80) cc_final: 0.8096 (m-80)
REVERT: B  687 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8388 (ptp)
REVERT: B  721 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8808 (mp10)
  outliers start: 27
  outliers final: 15
  residues processed: 111
  average time/residue: 1.3590
  time to fit residues: 167.5009
Evaluate side-chains
  109 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 1.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  687 MET
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  687 MET
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0670
   chunk 13 optimal weight:    1.9990
   chunk 99 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 133 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 114 optimal weight:    6.9990
   chunk 157 optimal weight:    9.9990
   overall best weight:    0.9322

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.086076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.049373 restraints weight = 28735.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.2691 rms_B_bonded: 2.65
r_work: 0.2575 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2461 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9064
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13256  Z= 0.121
  Angle     :  0.605  11.196  18030  Z= 0.292
  Chirality :  0.044   0.184   2002
  Planarity :  0.004   0.046   2382
  Dihedral  :  3.658  15.755   1820
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 19.25 %
    Favored  : 79.16 %
  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:  0.99 (0.21), residues: 1704
  helix:  1.48 (0.22), residues: 628
  sheet:  0.45 (0.32), residues: 256
  loop :  0.19 (0.23), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  40 
 HIS   0.002   0.000   HIS B  68 
 PHE   0.010   0.001   PHE A 682 
 TYR   0.020   0.002   TYR B 277 
 ARG   0.013   0.000   ARG A 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03922 (  532)
  hydrogen bonds       : angle       4.51917 ( 1452)
  covalent geometry    : bond        0.00288 (13256)
  covalent geometry    : angle       0.60456 (18030)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 14900.31 seconds
wall clock time: 256 minutes 34.88 seconds (15394.88 seconds total)