Starting phenix.real_space_refine
on Thu May 15 07:56:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b7z_44329/05_2025/9b7z_44329_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b7z_44329/05_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_44329/05_2025/9b7z_44329.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b7z_44329/05_2025/9b7z_44329.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b7z_44329/05_2025/9b7z_44329_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b7z_44329/05_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): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 14.63, per 1000 atoms: 1.13
  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: 3.02
  Conformation dependent library (CDL) restraints added in 1.7 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: 1.70
  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: 4.55

  Time building geometry restraints manager: 3.58 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.980
  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:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     38.410
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.210
-------------------------------------------------------------------------------
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  : 1.326 
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: 1.5397
  time to fit residues: 266.6041
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  : 1.340 
-------------------------------------------------------------------------------
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 = 59)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.049930 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: 0.2471 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9044
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  : 1.494 
Fit side-chains
REVERT: A  240 ARG cc_start: 0.9079 (mmt-90) cc_final: 0.8212 (mmm160)
REVERT: A  530 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7861 (t80)
REVERT: A  556 LEU cc_start: 0.9183 (mm) cc_final: 0.8960 (mp)
REVERT: A  611 LYS cc_start: 0.9101 (tttt) cc_final: 0.8896 (ptmt)
REVERT: A  680 MET cc_start: 0.9004 (tpp) cc_final: 0.8669 (mpp)
REVERT: A  682 PHE cc_start: 0.8656 (m-80) cc_final: 0.8358 (m-80)
REVERT: B  240 ARG cc_start: 0.9079 (mmt-90) cc_final: 0.8220 (mmm160)
REVERT: B  499 MET cc_start: 0.8831 (pmm) cc_final: 0.8544 (pmm)
REVERT: B  556 LEU cc_start: 0.9194 (mm) cc_final: 0.8969 (mp)
REVERT: B  611 LYS cc_start: 0.9091 (tttt) cc_final: 0.8874 (ptmt)
REVERT: B  680 MET cc_start: 0.9000 (tpp) cc_final: 0.8671 (mpp)
REVERT: B  682 PHE cc_start: 0.8687 (m-80) cc_final: 0.8471 (m-80)
REVERT: B  687 MET cc_start: 0.8300 (mtm) cc_final: 0.8080 (mtt)
  outliers start: 34
  outliers final: 14
  residues processed: 130
  average time/residue: 1.3293
  time to fit residues: 188.3654
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  : 1.358 
-------------------------------------------------------------------------------
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:    0.0870
   chunk 85 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9990
   chunk 139 optimal weight:   20.0000
   chunk 51 optimal weight:    5.9990
   chunk 118 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 135 optimal weight:    7.9990
   overall best weight:    1.3562

-------------------------------------------------------------------------------
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 = 0.3506 r_free = 0.3506 target = 0.085806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.048657 restraints weight = 29031.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.2673 rms_B_bonded: 2.65
r_work: 0.2553 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2436 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9071
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  13256  Z= 0.154
  Angle     :  0.601   8.015  18030  Z= 0.299
  Chirality :  0.044   0.158   2002
  Planarity :  0.005   0.048   2382
  Dihedral  :  4.620  50.443   1826
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.86 %
    Favored  : 80.97 %
  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:  0.16 (0.20), residues: 1704
  helix:  0.52 (0.21), residues: 618
  sheet:  0.60 (0.34), residues: 224
  loop : -0.24 (0.21), residues: 862

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 627 
 HIS   0.004   0.001   HIS A  68 
 PHE   0.012   0.001   PHE A 530 
 TYR   0.023   0.002   TYR B 277 
 ARG   0.003   0.000   ARG B 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05044 (  532)
  hydrogen bonds       : angle       4.99537 ( 1452)
  covalent geometry    : bond        0.00366 (13256)
  covalent geometry    : angle       0.60137 (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
  132 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 1.589 
Fit side-chains
REVERT: A  240 ARG cc_start: 0.9092 (mmt-90) cc_final: 0.8359 (mmm160)
REVERT: A  530 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7829 (t80)
REVERT: A  556 LEU cc_start: 0.9184 (mm) cc_final: 0.8950 (mp)
REVERT: A  573 ARG cc_start: 0.8742 (mmm-85) cc_final: 0.8357 (mmm160)
REVERT: A  611 LYS cc_start: 0.9099 (tttt) cc_final: 0.8853 (ptmt)
REVERT: A  680 MET cc_start: 0.9054 (tpp) cc_final: 0.8534 (mpp)
REVERT: A  721 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8878 (mp10)
REVERT: B  240 ARG cc_start: 0.9094 (mmt-90) cc_final: 0.8390 (mmm160)
REVERT: B  499 MET cc_start: 0.8810 (pmm) cc_final: 0.8568 (pmm)
REVERT: B  556 LEU cc_start: 0.9185 (mm) cc_final: 0.8953 (mp)
REVERT: B  573 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.8307 (mmm160)
REVERT: B  680 MET cc_start: 0.9106 (tpp) cc_final: 0.8665 (mpp)
REVERT: B  682 PHE cc_start: 0.8631 (m-80) cc_final: 0.8290 (m-80)
REVERT: B  687 MET cc_start: 0.8316 (mtm) cc_final: 0.8064 (mtt)
REVERT: B  721 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8868 (mp10)
  outliers start: 30
  outliers final: 15
  residues processed: 122
  average time/residue: 1.4402
  time to fit residues: 190.7325
Evaluate side-chains
  110 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 1.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  112 SER
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 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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 150 optimal weight:   10.0000
   chunk 72 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 162 optimal weight:    6.9990
   chunk 114 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   chunk 140 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   overall best weight:    2.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 331 HIS
** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 789 HIS
B 331 HIS
** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 789 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.083115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.045863 restraints weight = 28939.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.2598 rms_B_bonded: 2.63
r_work: 0.2475 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2359 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9125
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049  13256  Z= 0.285
  Angle     :  0.687   8.509  18030  Z= 0.344
  Chirality :  0.049   0.166   2002
  Planarity :  0.005   0.049   2382
  Dihedral  :  4.716  40.758   1826
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 16.35 %
    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:  0.20 (0.20), residues: 1704
  helix:  0.49 (0.20), residues: 622
  sheet:  0.55 (0.34), residues: 236
  loop : -0.13 (0.22), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  40 
 HIS   0.004   0.001   HIS A 789 
 PHE   0.014   0.002   PHE A  65 
 TYR   0.021   0.002   TYR A 222 
 ARG   0.004   0.001   ARG B 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06164 (  532)
  hydrogen bonds       : angle       5.08983 ( 1452)
  covalent geometry    : bond        0.00691 (13256)
  covalent geometry    : angle       0.68728 (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
  142 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 93
  time to evaluate  : 1.457 
Fit side-chains
REVERT: A   57 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9453 (mp)
REVERT: A  240 ARG cc_start: 0.9115 (mmt-90) cc_final: 0.7970 (mmm160)
REVERT: A  499 MET cc_start: 0.8868 (pmm) cc_final: 0.8033 (ptt)
REVERT: A  530 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7800 (t80)
REVERT: A  573 ARG cc_start: 0.8729 (mmm-85) cc_final: 0.8295 (mmm160)
REVERT: A  680 MET cc_start: 0.9098 (tpp) cc_final: 0.8428 (mpp)
REVERT: A  721 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8890 (mp10)
REVERT: B   57 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9449 (mp)
REVERT: B  240 ARG cc_start: 0.9103 (mmt-90) cc_final: 0.8112 (mmm160)
REVERT: B  530 PHE cc_start: 0.8135 (t80) cc_final: 0.7806 (t80)
REVERT: B  556 LEU cc_start: 0.9170 (mm) cc_final: 0.8968 (mp)
REVERT: B  573 ARG cc_start: 0.8699 (mmm-85) cc_final: 0.8260 (mmm160)
REVERT: B  680 MET cc_start: 0.9110 (tpp) cc_final: 0.8578 (mpp)
REVERT: B  721 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8889 (mp10)
  outliers start: 49
  outliers final: 18
  residues processed: 130
  average time/residue: 1.2639
  time to fit residues: 179.7737
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  : 1.479 
-------------------------------------------------------------------------------
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  112 SER
Chi-restraints excluded: chain A residue  196 THR
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  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  112 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  407 ASN
Chi-restraints excluded: chain B residue  527 VAL
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:    9.9990
   chunk 45 optimal weight:    0.6980
   chunk 153 optimal weight:   20.0000
   chunk 40 optimal weight:    2.9990
   chunk 152 optimal weight:    1.9990
   chunk 48 optimal weight:    0.1980
   chunk 32 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 162 optimal weight:    5.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3497 r_free = 0.3497 target = 0.085319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.048207 restraints weight = 29079.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.2663 rms_B_bonded: 2.67
r_work: 0.2542 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2427 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9081
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13256  Z= 0.125
  Angle     :  0.584   8.291  18030  Z= 0.285
  Chirality :  0.044   0.170   2002
  Planarity :  0.004   0.047   2382
  Dihedral  :  4.063  17.018   1820
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.95 %
    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:  1.04 (0.21), residues: 610
  sheet:  0.69 (0.34), residues: 224
  loop : -0.07 (0.22), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 627 
 HIS   0.003   0.000   HIS B  68 
 PHE   0.017   0.001   PHE A 682 
 TYR   0.021   0.002   TYR A 277 
 ARG   0.008   0.000   ARG B 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04445 (  532)
  hydrogen bonds       : angle       4.85944 ( 1452)
  covalent geometry    : bond        0.00293 (13256)
  covalent geometry    : angle       0.58399 (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
  127 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 91
  time to evaluate  : 1.375 
Fit side-chains
REVERT: A  240 ARG cc_start: 0.9057 (mmt-90) cc_final: 0.7981 (mmm160)
REVERT: A  465 MET cc_start: 0.9545 (OUTLIER) cc_final: 0.8779 (mtm)
REVERT: A  499 MET cc_start: 0.8746 (pmm) cc_final: 0.8059 (ptt)
REVERT: A  530 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7746 (t80)
REVERT: A  573 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.8313 (mmm160)
REVERT: A  680 MET cc_start: 0.9084 (tpp) cc_final: 0.8435 (mpp)
REVERT: A  682 PHE cc_start: 0.8561 (m-80) cc_final: 0.8260 (m-80)
REVERT: A  687 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8099 (ptp)
REVERT: A  721 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8794 (mp10)
REVERT: B  240 ARG cc_start: 0.9056 (mmt-90) cc_final: 0.7986 (mmm160)
REVERT: B  499 MET cc_start: 0.8769 (pmm) cc_final: 0.7890 (ptt)
REVERT: B  573 ARG cc_start: 0.8730 (mmm-85) cc_final: 0.8284 (mmm160)
REVERT: B  680 MET cc_start: 0.9101 (tpp) cc_final: 0.8504 (mpp)
REVERT: B  682 PHE cc_start: 0.8511 (m-80) cc_final: 0.8063 (m-80)
REVERT: B  687 MET cc_start: 0.8321 (ptp) cc_final: 0.7980 (ptp)
REVERT: B  721 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8816 (mp10)
  outliers start: 36
  outliers final: 19
  residues processed: 116
  average time/residue: 1.3538
  time to fit residues: 171.5556
Evaluate side-chains
  108 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 1.509 
-------------------------------------------------------------------------------
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  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  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   91 VAL
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  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
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:   10.0000
   chunk 161 optimal weight:    0.8980
   chunk 110 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 136 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 80 optimal weight:    0.0070
   chunk 101 optimal weight:    5.9990
   overall best weight:    1.1802

-------------------------------------------------------------------------------
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 = 0.3492 r_free = 0.3492 target = 0.085022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.047980 restraints weight = 29459.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.2631 rms_B_bonded: 2.66
r_work: 0.2500 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2379 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9080
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13256  Z= 0.137
  Angle     :  0.583   8.471  18030  Z= 0.284
  Chirality :  0.044   0.179   2002
  Planarity :  0.004   0.045   2382
  Dihedral  :  3.949  16.978   1820
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.66 %
    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:  0.70 (0.21), residues: 1704
  helix:  1.21 (0.22), residues: 610
  sheet:  0.49 (0.32), residues: 256
  loop :  0.00 (0.22), residues: 838

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   0.014   0.001   PHE A 682 
 TYR   0.021   0.002   TYR A 277 
 ARG   0.006   0.000   ARG A 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04536 (  532)
  hydrogen bonds       : angle       4.75573 ( 1452)
  covalent geometry    : bond        0.00325 (13256)
  covalent geometry    : angle       0.58303 (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
  134 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 96
  time to evaluate  : 1.579 
Fit side-chains
REVERT: A  240 ARG cc_start: 0.9084 (mmt-90) cc_final: 0.8003 (mmm160)
REVERT: A  465 MET cc_start: 0.9520 (OUTLIER) cc_final: 0.8741 (mtm)
REVERT: A  499 MET cc_start: 0.8719 (pmm) cc_final: 0.8034 (ptt)
REVERT: A  530 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7788 (t80)
REVERT: A  573 ARG cc_start: 0.8774 (mmm-85) cc_final: 0.8337 (mmm160)
REVERT: A  680 MET cc_start: 0.9089 (tpp) cc_final: 0.8458 (mpp)
REVERT: A  682 PHE cc_start: 0.8533 (m-80) cc_final: 0.8145 (m-80)
REVERT: A  687 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8166 (ptp)
REVERT: A  721 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8807 (mp10)
REVERT: B  240 ARG cc_start: 0.9079 (mmt-90) cc_final: 0.7999 (mmm160)
REVERT: B  465 MET cc_start: 0.9515 (OUTLIER) cc_final: 0.8733 (mtm)
REVERT: B  499 MET cc_start: 0.8713 (pmm) cc_final: 0.7901 (ptt)
REVERT: B  573 ARG cc_start: 0.8770 (mmm-85) cc_final: 0.8319 (mmm160)
REVERT: B  680 MET cc_start: 0.9075 (tpp) cc_final: 0.8503 (mpp)
REVERT: B  682 PHE cc_start: 0.8522 (m-80) cc_final: 0.8122 (m-80)
REVERT: B  687 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7987 (ptp)
REVERT: B  721 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8820 (mp10)
  outliers start: 38
  outliers final: 17
  residues processed: 121
  average time/residue: 1.3345
  time to fit residues: 176.4707
Evaluate side-chains
  108 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 1.512 
-------------------------------------------------------------------------------
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  702 ILE
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain B residue   18 ASN
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  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
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:    1.9990
   chunk 153 optimal weight:    9.9990
   chunk 3 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9980
   chunk 150 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 156 optimal weight:    6.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 746 GLN
B 737 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.084549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.047619 restraints weight = 29010.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.2638 rms_B_bonded: 2.63
r_work: 0.2514 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2398 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9096
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13256  Z= 0.160
  Angle     :  0.596   8.734  18030  Z= 0.292
  Chirality :  0.045   0.171   2002
  Planarity :  0.005   0.045   2382
  Dihedral  :  3.995  17.353   1820
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.95 %
    Favored  : 79.23 %
  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:  0.73 (0.21), residues: 1704
  helix:  1.24 (0.22), residues: 612
  sheet:  0.53 (0.32), residues: 256
  loop : -0.00 (0.22), residues: 836

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  40 
 HIS   0.002   0.001   HIS B  68 
 PHE   0.013   0.001   PHE A 682 
 TYR   0.021   0.002   TYR B 277 
 ARG   0.011   0.000   ARG B 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04708 (  532)
  hydrogen bonds       : angle       4.74308 ( 1452)
  covalent geometry    : bond        0.00387 (13256)
  covalent geometry    : angle       0.59644 (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
  131 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 92
  time to evaluate  : 1.470 
Fit side-chains
REVERT: A  240 ARG cc_start: 0.9076 (mmt-90) cc_final: 0.7986 (mmm160)
REVERT: A  465 MET cc_start: 0.9527 (OUTLIER) cc_final: 0.8726 (mtm)
REVERT: A  499 MET cc_start: 0.8728 (pmm) cc_final: 0.8050 (ptt)
REVERT: A  530 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7796 (t80)
REVERT: A  573 ARG cc_start: 0.8778 (mmm-85) cc_final: 0.8354 (mmm160)
REVERT: A  680 MET cc_start: 0.9068 (tpp) cc_final: 0.8488 (mpp)
REVERT: A  682 PHE cc_start: 0.8474 (m-80) cc_final: 0.8059 (m-80)
REVERT: A  687 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8271 (ptp)
REVERT: A  721 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8813 (mp10)
REVERT: A  825 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8674 (ptt90)
REVERT: B  240 ARG cc_start: 0.9067 (mmt-90) cc_final: 0.7981 (mmm160)
REVERT: B  465 MET cc_start: 0.9527 (OUTLIER) cc_final: 0.8754 (mtm)
REVERT: B  499 MET cc_start: 0.8727 (pmm) cc_final: 0.7961 (ptt)
REVERT: B  573 ARG cc_start: 0.8780 (mmm-85) cc_final: 0.8358 (mmm160)
REVERT: B  680 MET cc_start: 0.9058 (tpp) cc_final: 0.8506 (mpp)
REVERT: B  682 PHE cc_start: 0.8482 (m-80) cc_final: 0.8048 (m-80)
REVERT: B  687 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7871 (ptp)
REVERT: B  721 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8823 (mp10)
REVERT: B  825 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8676 (ptt90)
  outliers start: 39
  outliers final: 18
  residues processed: 121
  average time/residue: 1.2080
  time to fit residues: 160.9598
Evaluate side-chains
  114 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 87
  time to evaluate  : 1.408 
-------------------------------------------------------------------------------
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  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  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  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  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
Chi-restraints excluded: chain B residue  825 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 67 optimal weight:    7.9990
   chunk 105 optimal weight:    2.9990
   chunk 161 optimal weight:    0.6980
   chunk 138 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 70 optimal weight:    9.9990
   chunk 119 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 746 GLN
** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 746 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.085721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.048965 restraints weight = 29002.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.2683 rms_B_bonded: 2.63
r_work: 0.2565 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2449 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9072
moved from start:          0.2775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  13256  Z= 0.112
  Angle     :  0.585  11.428  18030  Z= 0.284
  Chirality :  0.044   0.187   2002
  Planarity :  0.004   0.046   2382
  Dihedral  :  3.837  15.762   1820
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.87 %
    Favored  : 79.38 %
  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:  0.85 (0.21), residues: 1704
  helix:  1.41 (0.22), residues: 614
  sheet:  0.41 (0.32), residues: 260
  loop :  0.07 (0.23), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  40 
 HIS   0.002   0.000   HIS B  68 
 PHE   0.013   0.001   PHE A 682 
 TYR   0.021   0.002   TYR A 277 
 ARG   0.012   0.000   ARG B 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04029 (  532)
  hydrogen bonds       : angle       4.63585 ( 1452)
  covalent geometry    : bond        0.00266 (13256)
  covalent geometry    : angle       0.58529 (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
  132 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 94
  time to evaluate  : 1.385 
Fit side-chains
   revert: symmetry clash
REVERT: A  240 ARG cc_start: 0.9051 (mmt-90) cc_final: 0.8001 (mmm160)
REVERT: A  499 MET cc_start: 0.8705 (pmm) cc_final: 0.8068 (ptt)
REVERT: A  530 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7824 (t80)
REVERT: A  573 ARG cc_start: 0.8809 (mmm-85) cc_final: 0.8388 (mmm160)
REVERT: A  680 MET cc_start: 0.9051 (tpp) cc_final: 0.8511 (mpp)
REVERT: A  682 PHE cc_start: 0.8435 (m-80) cc_final: 0.8105 (m-80)
REVERT: A  687 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8316 (ptp)
REVERT: A  721 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8804 (mp10)
REVERT: A  772 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.9242 (tptm)
REVERT: B  240 ARG cc_start: 0.9048 (mmt-90) cc_final: 0.8003 (mmm160)
REVERT: B  465 MET cc_start: 0.9513 (OUTLIER) cc_final: 0.8735 (mtm)
REVERT: B  499 MET cc_start: 0.8743 (pmm) cc_final: 0.8020 (ptt)
REVERT: B  573 ARG cc_start: 0.8812 (mmm-85) cc_final: 0.8395 (mmm160)
REVERT: B  680 MET cc_start: 0.9059 (tpp) cc_final: 0.8534 (mpp)
REVERT: B  682 PHE cc_start: 0.8477 (m-80) cc_final: 0.8168 (m-80)
REVERT: B  687 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7918 (ptp)
REVERT: B  721 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8807 (mp10)
  outliers start: 38
  outliers final: 19
  residues processed: 123
  average time/residue: 1.2521
  time to fit residues: 171.8663
Evaluate side-chains
  113 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 1.530 
-------------------------------------------------------------------------------
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  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  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 A residue  772 LYS
Chi-restraints excluded: chain B residue   30 VAL
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  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:    1.9990
   chunk 148 optimal weight:    0.0980
   chunk 169 optimal weight:    3.9990
   chunk 110 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9980
   chunk 106 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3487 r_free = 0.3487 target = 0.084678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.047645 restraints weight = 29041.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.2644 rms_B_bonded: 2.67
r_work: 0.2522 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2404 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9088
moved from start:          0.2773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13256  Z= 0.154
  Angle     :  0.619  10.933  18030  Z= 0.302
  Chirality :  0.045   0.186   2002
  Planarity :  0.005   0.045   2382
  Dihedral  :  3.906  16.327   1820
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.09 %
    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:  0.78 (0.21), residues: 1704
  helix:  1.24 (0.22), residues: 628
  sheet:  0.50 (0.32), residues: 256
  loop :  0.08 (0.23), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  40 
 HIS   0.002   0.001   HIS B 331 
 PHE   0.012   0.001   PHE A 682 
 TYR   0.021   0.002   TYR B 277 
 ARG   0.011   0.000   ARG A 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04575 (  532)
  hydrogen bonds       : angle       4.66437 ( 1452)
  covalent geometry    : bond        0.00370 (13256)
  covalent geometry    : angle       0.61902 (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
  125 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 91
  time to evaluate  : 1.424 
Fit side-chains
REVERT: A  240 ARG cc_start: 0.9069 (mmt-90) cc_final: 0.7937 (mmm160)
REVERT: A  465 MET cc_start: 0.9521 (OUTLIER) cc_final: 0.8740 (mtm)
REVERT: A  499 MET cc_start: 0.8718 (pmm) cc_final: 0.8090 (ptt)
REVERT: A  530 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7845 (t80)
REVERT: A  573 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.8386 (mmm160)
REVERT: A  680 MET cc_start: 0.9049 (tpp) cc_final: 0.8500 (mpp)
REVERT: A  682 PHE cc_start: 0.8402 (m-80) cc_final: 0.8051 (m-80)
REVERT: A  687 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8147 (ptp)
REVERT: A  721 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8808 (mp10)
REVERT: B  240 ARG cc_start: 0.9065 (mmt-90) cc_final: 0.7931 (mmm160)
REVERT: B  465 MET cc_start: 0.9520 (OUTLIER) cc_final: 0.8738 (mtm)
REVERT: B  499 MET cc_start: 0.8760 (pmm) cc_final: 0.8089 (ptt)
REVERT: B  573 ARG cc_start: 0.8805 (mmm-85) cc_final: 0.8382 (mmm160)
REVERT: B  680 MET cc_start: 0.9056 (tpp) cc_final: 0.8531 (mpp)
REVERT: B  682 PHE cc_start: 0.8468 (m-80) cc_final: 0.8140 (m-80)
REVERT: B  687 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7931 (ptp)
REVERT: B  721 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8810 (mp10)
  outliers start: 34
  outliers final: 18
  residues processed: 115
  average time/residue: 1.1558
  time to fit residues: 147.2597
Evaluate side-chains
  112 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
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  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  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  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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 131 optimal weight:    0.9980
   chunk 86 optimal weight:    0.1980
   chunk 62 optimal weight:    9.9990
   chunk 59 optimal weight:    0.0970
   chunk 48 optimal weight:    0.8980
   chunk 163 optimal weight:    2.9990
   chunk 70 optimal weight:    9.9990
   chunk 46 optimal weight:    0.7980
   chunk 160 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 328 ASN
A 746 GLN
B 328 ASN
B 746 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.086219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.049767 restraints weight = 28847.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.2711 rms_B_bonded: 2.65
r_work: 0.2593 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2482 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9074
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  13256  Z= 0.103
  Angle     :  0.588  10.415  18030  Z= 0.283
  Chirality :  0.044   0.193   2002
  Planarity :  0.004   0.046   2382
  Dihedral  :  3.710  16.031   1820
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.67 %
    Favored  : 79.38 %
  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:  0.97 (0.21), residues: 1704
  helix:  1.54 (0.22), residues: 616
  sheet:  0.40 (0.32), residues: 260
  loop :  0.14 (0.23), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  40 
 HIS   0.002   0.000   HIS A 580 
 PHE   0.013   0.001   PHE A 682 
 TYR   0.021   0.002   TYR B 277 
 ARG   0.016   0.000   ARG B 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03659 (  532)
  hydrogen bonds       : angle       4.53817 ( 1452)
  covalent geometry    : bond        0.00236 (13256)
  covalent geometry    : angle       0.58821 (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
  119 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 1.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 ARG cc_start: 0.9017 (mmt-90) cc_final: 0.8047 (mmm160)
REVERT: A  465 MET cc_start: 0.9502 (OUTLIER) cc_final: 0.8678 (mtm)
REVERT: A  499 MET cc_start: 0.8677 (pmm) cc_final: 0.8012 (ptt)
REVERT: A  530 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7911 (t80)
REVERT: A  573 ARG cc_start: 0.8857 (mmm-85) cc_final: 0.8435 (mmm160)
REVERT: A  680 MET cc_start: 0.9052 (tpp) cc_final: 0.8535 (mpp)
REVERT: A  682 PHE cc_start: 0.8386 (m-80) cc_final: 0.8111 (m-80)
REVERT: A  687 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8150 (ptp)
REVERT: A  721 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8809 (mp10)
REVERT: A  746 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8392 (tp40)
REVERT: B  240 ARG cc_start: 0.9003 (mmt-90) cc_final: 0.8036 (mmm160)
REVERT: B  465 MET cc_start: 0.9508 (OUTLIER) cc_final: 0.8714 (mtm)
REVERT: B  499 MET cc_start: 0.8713 (pmm) cc_final: 0.8003 (ptt)
REVERT: B  530 PHE cc_start: 0.8192 (t80) cc_final: 0.7706 (t80)
REVERT: B  573 ARG cc_start: 0.8838 (mmm-85) cc_final: 0.8412 (mmm160)
REVERT: B  680 MET cc_start: 0.9062 (tpp) cc_final: 0.8567 (mpp)
REVERT: B  682 PHE cc_start: 0.8443 (m-80) cc_final: 0.8109 (m-80)
REVERT: B  687 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8010 (ptp)
REVERT: B  721 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8808 (mp10)
REVERT: B  746 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8283 (tp40)
  outliers start: 27
  outliers final: 16
  residues processed: 113
  average time/residue: 1.1850
  time to fit residues: 147.3981
Evaluate side-chains
  113 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
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  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  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  746 GLN
Chi-restraints excluded: chain B residue   30 VAL
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  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
Chi-restraints excluded: chain B residue  746 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 46 optimal weight:    0.3980
   chunk 17 optimal weight:    2.9990
   chunk 133 optimal weight:    2.9990
   chunk 1 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 114 optimal weight:    5.9990
   chunk 157 optimal weight:    9.9990
   overall best weight:    1.1584

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.086233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.049807 restraints weight = 28635.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.2711 rms_B_bonded: 2.65
r_work: 0.2591 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2479 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9072
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.190  13256  Z= 0.229
  Angle     :  1.070  59.178  18030  Z= 0.608
  Chirality :  0.044   0.182   2002
  Planarity :  0.004   0.046   2382
  Dihedral  :  3.710  15.995   1820
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.81 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.13 %
  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:  0.98 (0.21), residues: 1704
  helix:  1.54 (0.22), residues: 616
  sheet:  0.40 (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 B  40 
 HIS   0.002   0.000   HIS A 580 
 PHE   0.012   0.001   PHE A 682 
 TYR   0.021   0.002   TYR B 277 
 ARG   0.012   0.000   ARG B 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03698 (  532)
  hydrogen bonds       : angle       4.53877 ( 1452)
  covalent geometry    : bond        0.00482 (13256)
  covalent geometry    : angle       1.07047 (18030)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12617.28 seconds
wall clock time: 217 minutes 0.72 seconds (13020.72 seconds total)