Starting phenix.real_space_refine
on Tue Dec 31 11:04:32 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uid_42293/12_2024/8uid_42293.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uid_42293/12_2024/8uid_42293.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uid_42293/12_2024/8uid_42293.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uid_42293/12_2024/8uid_42293.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uid_42293/12_2024/8uid_42293.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uid_42293/12_2024/8uid_42293.cif"
  }
  resolution = 2.81
  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=  -0.002 sd=   0.276
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      44      5.16       5
     C   10098      2.51       5
     N    2628      2.21       5
     O    2868      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 76 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 15638
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 738, 5968
          Classifications: {'peptide': 738}
          Link IDs: {'CIS': 1, 'PTRANS': 35, 'TRANS': 701}
    Chain: "B"
      Number of atoms: 1851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1851
          Classifications: {'peptide': 227}
          Link IDs: {'PTRANS': 14, 'TRANS': 212}
  Restraints were copied for chains:
    C, D
  Time building chain proxies: 14.54, per 1000 atoms: 0.93
  Number of scatterers: 15638
  At special positions: 0
  Unit cell: (105.78, 128.14, 86.86, 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      44     16.00
     O    2868      8.00
     N    2628      7.00
     C   10098      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.56
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3540

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 28 sheets defined
      20.3% alpha, 31.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 16
      No H-bonds generated for 'chain 'A' and resid 14 through 16'
    Processing helix  chain 'A' and resid 17 through 28
    Processing helix  chain 'A' and resid 38 through 43
    Processing helix  chain 'A' and resid 67 through 78
    Processing helix  chain 'A' and resid 94 through 99
    Processing helix  chain 'A' and resid 102 through 107
      removed outlier: 3.785A  pdb=" N   LYS A 106 " --> pdb=" O   TRP A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 138
      removed outlier: 3.504A  pdb=" N   LYS A 119 " --> pdb=" O   PRO A 115 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   HIS A 120 " --> pdb=" O   GLY A 116 " (cutoff:3.500A)
      Proline residue:  A 134  - end of helix
    Processing helix  chain 'A' and resid 154 through 169
      removed outlier: 3.660A  pdb=" N   ILE A 158 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 211
      removed outlier: 3.559A  pdb=" N   PHE A 201 " --> pdb=" O   ASP A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 258
      removed outlier: 3.547A  pdb=" N   THR A 247 " --> pdb=" O   PRO A 243 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLU A 248 " --> pdb=" O   PRO A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 314
      removed outlier: 3.588A  pdb=" N   TYR A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 320
      removed outlier: 3.541A  pdb=" N   SER A 320 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 489
    Processing helix  chain 'A' and resid 598 through 603
    Processing helix  chain 'A' and resid 619 through 625
    Processing helix  chain 'A' and resid 722 through 729
    Processing helix  chain 'A' and resid 731 through 738
      removed outlier: 3.981A  pdb=" N   LYS A 735 " --> pdb=" O   GLU A 731 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 804 through 807
      removed outlier: 3.524A  pdb=" N   LEU B 807 " --> pdb=" O   THR B 804 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 804 through 807'
    Processing helix  chain 'B' and resid 844 through 849
    Processing helix  chain 'B' and resid 850 through 855
    Processing helix  chain 'B' and resid 868 through 871
    Processing helix  chain 'C' and resid 14 through 16
      No H-bonds generated for 'chain 'C' and resid 14 through 16'
    Processing helix  chain 'C' and resid 17 through 28
    Processing helix  chain 'C' and resid 38 through 43
    Processing helix  chain 'C' and resid 67 through 78
    Processing helix  chain 'C' and resid 94 through 99
    Processing helix  chain 'C' and resid 102 through 107
      removed outlier: 3.785A  pdb=" N   LYS C 106 " --> pdb=" O   TRP C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 138
      removed outlier: 3.504A  pdb=" N   LYS C 119 " --> pdb=" O   PRO C 115 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   HIS C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      Proline residue:  C 134  - end of helix
    Processing helix  chain 'C' and resid 154 through 169
      removed outlier: 3.660A  pdb=" N   ILE C 158 " --> pdb=" O   ASN C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 211
      removed outlier: 3.561A  pdb=" N   PHE C 201 " --> pdb=" O   ASP C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 243 through 258
      removed outlier: 3.547A  pdb=" N   THR C 247 " --> pdb=" O   PRO C 243 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLU C 248 " --> pdb=" O   PRO C 244 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 314
      removed outlier: 3.588A  pdb=" N   TYR C 302 " --> pdb=" O   SER C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 314 through 320
      removed outlier: 3.542A  pdb=" N   SER C 320 " --> pdb=" O   GLU C 316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 484 through 489
    Processing helix  chain 'C' and resid 598 through 603
    Processing helix  chain 'C' and resid 619 through 625
    Processing helix  chain 'C' and resid 722 through 729
    Processing helix  chain 'C' and resid 731 through 738
      removed outlier: 3.981A  pdb=" N   LYS C 735 " --> pdb=" O   GLU C 731 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 804 through 807
      removed outlier: 3.523A  pdb=" N   LEU D 807 " --> pdb=" O   THR D 804 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 804 through 807'
    Processing helix  chain 'D' and resid 844 through 849
    Processing helix  chain 'D' and resid 850 through 855
    Processing helix  chain 'D' and resid 868 through 871
    Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 175
      removed outlier: 3.788A  pdb=" N   LEU A 173 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   VAL A  82 " --> pdb=" O   GLY A 143 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   GLN A 145 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ALA A  84 " --> pdb=" O   GLN A 145 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   VAL A  33 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   ARG A  85 " --> pdb=" O   VAL A  33 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   THR A  35 " --> pdb=" O   ARG A  85 " (cutoff:3.500A)
      removed outlier: 5.897A  pdb=" N   LEU A   4 " --> pdb=" O   CYS A  32 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   SER A  34 " --> pdb=" O   LEU A   4 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   GLY A   6 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   TYR A  36 " --> pdb=" O   GLY A   6 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   GLU A   7 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET A 266 " --> pdb=" O   GLU A   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 328 through 329
    Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 340
      removed outlier: 3.879A  pdb=" N   LEU A 385 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   VAL A 398 " --> pdb=" O   ASP A 387 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   VAL A 389 " --> pdb=" O   LYS A 396 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   LYS A 396 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ALA A 429 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   THR A 400 " --> pdb=" O   GLU A 427 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   GLU A 427 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 359
    Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 410
      removed outlier: 5.635A  pdb=" N   ALA A 404 " --> pdb=" O   TYR A 419 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   TYR A 419 " --> pdb=" O   ALA A 404 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A 406 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL A 414 " --> pdb=" O   LEU A 478 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   ILE A 480 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   MET A 416 " --> pdb=" O   ILE A 480 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   THR A 482 " --> pdb=" O   MET A 416 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   ILE A 418 " --> pdb=" O   THR A 482 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASP A 438 " --> pdb=" O   LYS A 470 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 490 through 494
      removed outlier: 6.435A  pdb=" N   LEU A 497 " --> pdb=" O   VAL A 493 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL A 557 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 509 through 510
      removed outlier: 3.541A  pdb=" N   ALA A 540 " --> pdb=" O   LYS B 971 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   ILE A 541 " --> pdb=" O   LEU A 548 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 573 through 574
    Processing sheet with id=AA9, first strand: chain 'A' and resid 573 through 574
      removed outlier: 5.151A  pdb=" N   ILE B 952 " --> pdb=" O   TRP B 900 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   TRP B 900 " --> pdb=" O   ILE B 952 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   VAL B 893 " --> pdb=" O   VAL B 927 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 859 through 861
      removed outlier: 4.194A  pdb=" N   TYR A 579 " --> pdb=" O   ALA B 861 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY B 914 " --> pdb=" O   VAL B 906 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   VAL B 908 " --> pdb=" O   PHE B 912 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   PHE B 912 " --> pdb=" O   VAL B 908 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 591 through 593
      removed outlier: 3.924A  pdb=" N   TRP B 838 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLU B 837 " --> pdb=" O   ARG A 615 " (cutoff:3.500A)
      removed outlier: 5.802A  pdb=" N   ILE A 644 " --> pdb=" O   TYR A 648 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   TYR A 648 " --> pdb=" O   ILE A 644 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 655 through 659
      removed outlier: 6.926A  pdb=" N   PHE A 636 " --> pdb=" O   TYR A 692 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   TYR A 692 " --> pdb=" O   PHE A 636 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TYR B 832 " --> pdb=" O   LEU A 697 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704
      removed outlier: 3.514A  pdb=" N   GLY A 701 " --> pdb=" O   VAL B 829 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 709 through 710
      removed outlier: 6.219A  pdb=" N   VAL B 789 " --> pdb=" O   TYR B 793 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   TYR B 793 " --> pdb=" O   VAL B 789 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 173 through 175
      removed outlier: 3.787A  pdb=" N   LEU C 173 " --> pdb=" O   ILE C 142 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   VAL C  82 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   GLN C 145 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ALA C  84 " --> pdb=" O   GLN C 145 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   VAL C  33 " --> pdb=" O   ILE C  83 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   ARG C  85 " --> pdb=" O   VAL C  33 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   THR C  35 " --> pdb=" O   ARG C  85 " (cutoff:3.500A)
      removed outlier: 5.898A  pdb=" N   LEU C   4 " --> pdb=" O   CYS C  32 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   SER C  34 " --> pdb=" O   LEU C   4 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   GLY C   6 " --> pdb=" O   SER C  34 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   TYR C  36 " --> pdb=" O   GLY C   6 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   GLU C   7 " --> pdb=" O   ILE C 264 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET C 266 " --> pdb=" O   GLU C   7 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 328 through 329
    Processing sheet with id=AB8, first strand: chain 'C' and resid 335 through 340
      removed outlier: 3.880A  pdb=" N   LEU C 385 " --> pdb=" O   THR C 400 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   VAL C 398 " --> pdb=" O   ASP C 387 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL C 389 " --> pdb=" O   LYS C 396 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LYS C 396 " --> pdb=" O   VAL C 389 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ALA C 429 " --> pdb=" O   VAL C 398 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   THR C 400 " --> pdb=" O   GLU C 427 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   GLU C 427 " --> pdb=" O   THR C 400 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 357 through 359
    Processing sheet with id=AC1, first strand: chain 'C' and resid 403 through 410
      removed outlier: 5.635A  pdb=" N   ALA C 404 " --> pdb=" O   TYR C 419 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   TYR C 419 " --> pdb=" O   ALA C 404 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU C 406 " --> pdb=" O   ILE C 417 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL C 414 " --> pdb=" O   LEU C 478 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   ILE C 480 " --> pdb=" O   VAL C 414 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   MET C 416 " --> pdb=" O   ILE C 480 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   THR C 482 " --> pdb=" O   MET C 416 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ILE C 418 " --> pdb=" O   THR C 482 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASP C 438 " --> pdb=" O   LYS C 470 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 490 through 494
      removed outlier: 6.435A  pdb=" N   LEU C 497 " --> pdb=" O   VAL C 493 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL C 557 " --> pdb=" O   LEU C 553 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 509 through 510
      removed outlier: 3.542A  pdb=" N   ALA C 540 " --> pdb=" O   LYS D 971 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ILE C 541 " --> pdb=" O   LEU C 548 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 573 through 574
    Processing sheet with id=AC5, first strand: chain 'C' and resid 573 through 574
      removed outlier: 5.150A  pdb=" N   ILE D 952 " --> pdb=" O   TRP D 900 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   TRP D 900 " --> pdb=" O   ILE D 952 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   VAL D 893 " --> pdb=" O   VAL D 927 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 859 through 861
      removed outlier: 4.194A  pdb=" N   TYR C 579 " --> pdb=" O   ALA D 861 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY D 914 " --> pdb=" O   VAL D 906 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   VAL D 908 " --> pdb=" O   PHE D 912 " (cutoff:3.500A)
      removed outlier: 5.390A  pdb=" N   PHE D 912 " --> pdb=" O   VAL D 908 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'C' and resid 591 through 593
      removed outlier: 3.924A  pdb=" N   TRP D 838 " --> pdb=" O   ILE C 593 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLU D 837 " --> pdb=" O   ARG C 615 " (cutoff:3.500A)
      removed outlier: 5.802A  pdb=" N   ILE C 644 " --> pdb=" O   TYR C 648 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   TYR C 648 " --> pdb=" O   ILE C 644 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'C' and resid 655 through 659
      removed outlier: 6.927A  pdb=" N   PHE C 636 " --> pdb=" O   TYR C 692 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   TYR C 692 " --> pdb=" O   PHE C 636 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TYR D 832 " --> pdb=" O   LEU C 697 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'C' and resid 701 through 704
      removed outlier: 3.515A  pdb=" N   GLY C 701 " --> pdb=" O   VAL D 829 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 709 through 710
      removed outlier: 6.219A  pdb=" N   VAL D 789 " --> pdb=" O   TYR D 793 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   TYR D 793 " --> pdb=" O   VAL D 789 " (cutoff:3.500A)

    600 hydrogen bonds defined for protein.
    1584 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: 7.26

  Time building geometry restraints manager: 5.25 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3902
        1.33 -     1.45: 3313
        1.45 -     1.58: 8763
        1.58 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 16044
  Sorted by residual:
  bond pdb=" CZ  ARG C 111 "
       pdb=" NH2 ARG C 111 "
    ideal  model  delta    sigma   weight residual
    1.330  1.284  0.046 1.30e-02 5.92e+03 1.23e+01
  bond pdb=" CA  LYS A 322 "
       pdb=" C   LYS A 322 "
    ideal  model  delta    sigma   weight residual
    1.518  1.551 -0.033 9.60e-03 1.09e+04 1.20e+01
  bond pdb=" CA  LYS C 322 "
       pdb=" C   LYS C 322 "
    ideal  model  delta    sigma   weight residual
    1.518  1.551 -0.033 9.60e-03 1.09e+04 1.18e+01
  bond pdb=" CZ  ARG A 111 "
       pdb=" NH2 ARG A 111 "
    ideal  model  delta    sigma   weight residual
    1.330  1.285  0.045 1.30e-02 5.92e+03 1.18e+01
  bond pdb=" CZ  ARG C 300 "
       pdb=" NH2 ARG C 300 "
    ideal  model  delta    sigma   weight residual
    1.330  1.286  0.044 1.30e-02 5.92e+03 1.16e+01
  ... (remaining 16039 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 17838
        2.46 -     4.92: 3660
        4.92 -     7.37: 285
        7.37 -     9.83: 29
        9.83 -    12.29: 2
  Bond angle restraints: 21814
  Sorted by residual:
  angle pdb=" CA  LYS C 322 "
        pdb=" C   LYS C 322 "
        pdb=" N   PRO C 323 "
      ideal   model   delta    sigma   weight residual
     117.68  123.08   -5.40 7.10e-01 1.98e+00 5.79e+01
  angle pdb=" CA  LYS A 322 "
        pdb=" C   LYS A 322 "
        pdb=" N   PRO A 323 "
      ideal   model   delta    sigma   weight residual
     117.68  123.06   -5.38 7.10e-01 1.98e+00 5.74e+01
  angle pdb=" CA  ARG A 239 "
        pdb=" C   ARG A 239 "
        pdb=" N   LEU A 240 "
      ideal   model   delta    sigma   weight residual
     118.38  127.40   -9.02 1.30e+00 5.92e-01 4.82e+01
  angle pdb=" CA  ARG C 239 "
        pdb=" C   ARG C 239 "
        pdb=" N   LEU C 240 "
      ideal   model   delta    sigma   weight residual
     118.38  127.40   -9.02 1.30e+00 5.92e-01 4.81e+01
  angle pdb=" C   ARG A 239 "
        pdb=" N   LEU A 240 "
        pdb=" CA  LEU A 240 "
      ideal   model   delta    sigma   weight residual
     121.70  133.99  -12.29 1.80e+00 3.09e-01 4.66e+01
  ... (remaining 21809 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 8309
       15.98 -    31.96: 851
       31.96 -    47.94: 196
       47.94 -    63.92: 70
       63.92 -    79.90: 30
  Dihedral angle restraints: 9456
    sinusoidal: 3866
      harmonic: 5590
  Sorted by residual:
  dihedral pdb=" C   ASP A 638 "
           pdb=" N   ASP A 638 "
           pdb=" CA  ASP A 638 "
           pdb=" CB  ASP A 638 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.65   17.05     0      2.50e+00 1.60e-01 4.65e+01
  dihedral pdb=" C   ASP C 638 "
           pdb=" N   ASP C 638 "
           pdb=" CA  ASP C 638 "
           pdb=" CB  ASP C 638 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.62   17.02     0      2.50e+00 1.60e-01 4.63e+01
  dihedral pdb=" CA  ASN C 148 "
           pdb=" C   ASN C 148 "
           pdb=" N   GLU C 149 "
           pdb=" CA  GLU C 149 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.63   29.37     0      5.00e+00 4.00e-02 3.45e+01
  ... (remaining 9453 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.148: 2017
       0.148 -    0.296: 332
       0.296 -    0.444: 25
       0.444 -    0.592: 4
       0.592 -    0.740: 2
  Chirality restraints: 2380
  Sorted by residual:
  chirality pdb=" CA  ASP A 638 "
            pdb=" N   ASP A 638 "
            pdb=" C   ASP A 638 "
            pdb=" CB  ASP A 638 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.77    0.74 2.00e-01 2.50e+01 1.37e+01
  chirality pdb=" CA  ASP C 638 "
            pdb=" N   ASP C 638 "
            pdb=" C   ASP C 638 "
            pdb=" CB  ASP C 638 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.77    0.74 2.00e-01 2.50e+01 1.37e+01
  chirality pdb=" CB  ILE D 939 "
            pdb=" CA  ILE D 939 "
            pdb=" CG1 ILE D 939 "
            pdb=" CG2 ILE D 939 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.12    0.52 2.00e-01 2.50e+01 6.78e+00
  ... (remaining 2377 not shown)

  Planarity restraints: 2780
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 196 "    0.182 2.00e-02 2.50e+03   9.21e-02 2.12e+02
        pdb=" CG  TRP C 196 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 196 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 196 "   -0.092 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 196 "   -0.049 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 196 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 196 "   -0.127 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 196 "    0.100 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 196 "   -0.031 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 196 "    0.103 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 196 "   -0.182 2.00e-02 2.50e+03   9.20e-02 2.12e+02
        pdb=" CG  TRP A 196 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 196 "    0.044 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 196 "    0.092 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 196 "    0.049 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 196 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 196 "    0.127 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 196 "   -0.099 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 196 "    0.030 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 196 "   -0.103 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  10 "    0.173 2.00e-02 2.50e+03   1.01e-01 2.03e+02
        pdb=" CG  TYR C  10 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  10 "   -0.081 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  10 "   -0.084 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  10 "   -0.075 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  10 "   -0.061 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  10 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR C  10 "    0.164 2.00e-02 2.50e+03
  ... (remaining 2777 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.38: 10
        2.38 -     3.01: 7893
        3.01 -     3.64: 23349
        3.64 -     4.27: 41477
        4.27 -     4.90: 67466
  Nonbonded interactions: 140195
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B 824 "
            pdb=" NH2 ARG C 360 "
     model   vdw
     1.749 3.200
  nonbonded pdb=" NH2 ARG A 360 "
            pdb=" ND2 ASN D 824 "
     model   vdw
     1.785 3.200
  nonbonded pdb=" OG  SER B 749 "
            pdb=" O   ALA C 330 "
     model   vdw
     1.895 3.040
  nonbonded pdb=" O   ALA A 330 "
            pdb=" OG  SER D 749 "
     model   vdw
     1.896 3.040
  nonbonded pdb=" NH2 ARG A 375 "
            pdb=" O   ARG C 231 "
     model   vdw
     2.133 3.120
  ... (remaining 140190 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             0.900
  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:          0.690
  Check model and map are aligned:         0.130
  Set scattering table:                    0.170
  Process input model:                     45.730
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   61.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
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      :  0.013   0.046  16044  Z= 0.823
  Angle     :  1.898  12.291  21814  Z= 1.249
  Chirality :  0.110   0.740   2380
  Planarity :  0.018   0.169   2780
  Dihedral  : 15.024  79.899   5916
  Min Nonbonded Distance : 1.749

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  :  6.82 %
    Favored  : 89.13 %
  Cbeta Deviations :  1.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -1.38 (0.17), residues: 1922
  helix: -1.81 (0.23), residues: 310
  sheet:  0.40 (0.24), residues: 404
  loop : -1.16 (0.17), residues: 1208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.182   0.024   TRP A 196 
 HIS   0.018   0.005   HIS A 460 
 PHE   0.082   0.019   PHE A 310 
 TYR   0.187   0.026   TYR A 235 
 ARG   0.014   0.002   ARG C  66 

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  388 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 319
  time to evaluate  : 1.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 SER cc_start: 0.8370 (m) cc_final: 0.7983 (t)
REVERT: A  218 MET cc_start: 0.8503 (ttt) cc_final: 0.8147 (ttp)
REVERT: A  355 ASN cc_start: 0.7681 (m-40) cc_final: 0.7434 (m110)
REVERT: B  840 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8060 (pp)
REVERT: B  885 LYS cc_start: 0.8184 (ptmm) cc_final: 0.7946 (ptmt)
REVERT: C  194 SER cc_start: 0.8380 (m) cc_final: 0.8010 (t)
REVERT: C  218 MET cc_start: 0.8511 (ttt) cc_final: 0.8151 (ttp)
REVERT: C  355 ASN cc_start: 0.7723 (m-40) cc_final: 0.7466 (m110)
REVERT: D  840 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8048 (pp)
REVERT: D  885 LYS cc_start: 0.8187 (ptmm) cc_final: 0.7961 (ptmt)
  outliers start: 69
  outliers final: 12
  residues processed: 375
  average time/residue: 1.5356
  time to fit residues: 629.6767
Evaluate side-chains
  181 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 167
  time to evaluate  : 2.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  552 ARG
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  840 ILE
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  552 ARG
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  840 ILE
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 160 optimal weight:    0.7980
   chunk 144 optimal weight:    0.9980
   chunk 79 optimal weight:   10.0000
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 148 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 90 optimal weight:    5.9990
   chunk 110 optimal weight:    1.9990
   chunk 172 optimal weight:    4.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
A 145 GLN
A 177 ASN
A 272 ASN
A 460 HIS
C  59 HIS
C 145 GLN
C 177 ASN
C 272 ASN
C 460 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16044  Z= 0.216
  Angle     :  0.679   9.551  21814  Z= 0.365
  Chirality :  0.050   0.221   2380
  Planarity :  0.005   0.048   2780
  Dihedral  :  7.313  58.260   2202
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 15.39 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.59 (0.19), residues: 1922
  helix: -0.20 (0.28), residues: 304
  sheet:  0.45 (0.24), residues: 472
  loop : -0.81 (0.18), residues: 1146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 152 
 HIS   0.005   0.001   HIS C  59 
 PHE   0.016   0.002   PHE D 788 
 TYR   0.028   0.002   TYR D 832 
 ARG   0.007   0.001   ARG B 934 

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 217
  time to evaluate  : 1.819 
Fit side-chains
REVERT: A  218 MET cc_start: 0.8497 (ttt) cc_final: 0.8164 (ttp)
REVERT: A  355 ASN cc_start: 0.7884 (m-40) cc_final: 0.7557 (p0)
REVERT: A  524 GLU cc_start: 0.6874 (pm20) cc_final: 0.6530 (pt0)
REVERT: B  859 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6827 (mp0)
REVERT: B  939 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7759 (mt)
REVERT: C  218 MET cc_start: 0.8503 (ttt) cc_final: 0.8173 (ttp)
REVERT: C  355 ASN cc_start: 0.7852 (m-40) cc_final: 0.7428 (p0)
REVERT: C  446 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.7767 (mt)
REVERT: C  524 GLU cc_start: 0.6862 (pm20) cc_final: 0.6532 (pt0)
REVERT: D  859 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6394 (mp0)
REVERT: D  939 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7768 (mt)
  outliers start: 68
  outliers final: 17
  residues processed: 262
  average time/residue: 1.4340
  time to fit residues: 413.7820
Evaluate side-chains
  177 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 1.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  859 GLU
Chi-restraints excluded: chain B residue  889 SER
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  591 THR
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  889 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 95 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 143 optimal weight:    4.9990
   chunk 117 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 172 optimal weight:    0.9990
   chunk 186 optimal weight:    0.1980
   chunk 153 optimal weight:    7.9990
   chunk 171 optimal weight:    0.9980
   chunk 58 optimal weight:    6.9990
   chunk 138 optimal weight:   10.0000
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 263 ASN
A 312 ASN
C 263 ASN
C 312 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  16044  Z= 0.278
  Angle     :  0.664   9.149  21814  Z= 0.350
  Chirality :  0.051   0.244   2380
  Planarity :  0.005   0.041   2780
  Dihedral  :  6.669  59.444   2188
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 16.10 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.52 (0.19), residues: 1922
  helix:  0.15 (0.29), residues: 304
  sheet:  0.33 (0.24), residues: 476
  loop : -0.76 (0.18), residues: 1142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 152 
 HIS   0.005   0.001   HIS A 460 
 PHE   0.013   0.002   PHE C 216 
 TYR   0.016   0.002   TYR C 639 
 ARG   0.005   0.001   ARG B 948 

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 162
  time to evaluate  : 1.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.5866 (mmt)
REVERT: A  446 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.7804 (mt)
REVERT: A  524 GLU cc_start: 0.7002 (pm20) cc_final: 0.6601 (pt0)
REVERT: B  939 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7774 (mt)
REVERT: C  446 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.7798 (mt)
REVERT: C  524 GLU cc_start: 0.6996 (pm20) cc_final: 0.6592 (pt0)
REVERT: D  859 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6502 (mp0)
REVERT: D  939 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7814 (mt)
  outliers start: 78
  outliers final: 25
  residues processed: 220
  average time/residue: 1.5171
  time to fit residues: 367.1669
Evaluate side-chains
  168 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 138
  time to evaluate  : 1.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  385 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  591 THR
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 170 optimal weight:    5.9990
   chunk 129 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 116 optimal weight:    5.9990
   chunk 173 optimal weight:    7.9990
   chunk 183 optimal weight:    0.4980
   chunk 90 optimal weight:    8.9990
   chunk 164 optimal weight:    7.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    1.8184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16044  Z= 0.272
  Angle     :  0.634   8.938  21814  Z= 0.333
  Chirality :  0.049   0.253   2380
  Planarity :  0.005   0.042   2780
  Dihedral  :  6.529  58.928   2188
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 18.63 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.50 (0.19), residues: 1922
  helix:  0.31 (0.29), residues: 304
  sheet:  0.17 (0.23), residues: 486
  loop : -0.71 (0.19), residues: 1132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 152 
 HIS   0.004   0.001   HIS A 460 
 PHE   0.011   0.002   PHE D 788 
 TYR   0.014   0.002   TYR C 639 
 ARG   0.005   0.000   ARG D 853 

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 151
  time to evaluate  : 1.865 
Fit side-chains
REVERT: A  108 MET cc_start: 0.6450 (OUTLIER) cc_final: 0.5920 (mmt)
REVERT: A  446 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.7823 (mt)
REVERT: B  859 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6569 (mp0)
REVERT: B  939 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7688 (mt)
REVERT: C  108 MET cc_start: 0.6544 (mpp) cc_final: 0.6037 (mmt)
REVERT: C  355 ASN cc_start: 0.7946 (m-40) cc_final: 0.7620 (m-40)
REVERT: D  939 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7729 (mt)
  outliers start: 69
  outliers final: 30
  residues processed: 205
  average time/residue: 1.2986
  time to fit residues: 295.9484
Evaluate side-chains
  166 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 132
  time to evaluate  : 1.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  848 ILE
Chi-restraints excluded: chain B residue  888 THR
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  531 LEU
Chi-restraints excluded: chain C residue  535 SER
Chi-restraints excluded: chain C residue  591 THR
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  848 ILE
Chi-restraints excluded: chain D residue  888 THR
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 152 optimal weight:    0.8980
   chunk 104 optimal weight:    0.4980
   chunk 2 optimal weight:    4.9990
   chunk 136 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 156 optimal weight:    4.9990
   chunk 126 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 93 optimal weight:    2.9990
   chunk 164 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 476 ASN
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 476 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  16044  Z= 0.259
  Angle     :  0.616   8.782  21814  Z= 0.324
  Chirality :  0.049   0.258   2380
  Planarity :  0.004   0.040   2780
  Dihedral  :  6.347  58.835   2188
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 18.74 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.52 (0.19), residues: 1922
  helix:  0.44 (0.30), residues: 306
  sheet:  0.09 (0.23), residues: 486
  loop : -0.74 (0.19), residues: 1130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 152 
 HIS   0.004   0.001   HIS C 460 
 PHE   0.012   0.002   PHE B 788 
 TYR   0.014   0.002   TYR C 639 
 ARG   0.005   0.000   ARG D 853 

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 146
  time to evaluate  : 1.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.6444 (mpp) cc_final: 0.5968 (mmt)
REVERT: A  109 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7421 (ptp-170)
REVERT: A  355 ASN cc_start: 0.7956 (m-40) cc_final: 0.7630 (m-40)
REVERT: A  446 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7771 (mt)
REVERT: B  859 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6535 (mp0)
REVERT: C  108 MET cc_start: 0.6556 (mpp) cc_final: 0.6030 (mmt)
REVERT: C  355 ASN cc_start: 0.7998 (m-40) cc_final: 0.7690 (m-40)
REVERT: C  427 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7215 (tt0)
REVERT: C  446 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7790 (mt)
REVERT: C  583 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7373 (tt0)
REVERT: C  615 ARG cc_start: 0.7246 (mtt-85) cc_final: 0.7037 (mtt-85)
REVERT: C  669 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6838 (mm-30)
REVERT: D  859 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6512 (mp0)
  outliers start: 76
  outliers final: 29
  residues processed: 201
  average time/residue: 1.2994
  time to fit residues: 291.1528
Evaluate side-chains
  167 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 132
  time to evaluate  : 1.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  848 ILE
Chi-restraints excluded: chain B residue  888 THR
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  427 GLU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  531 LEU
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  583 GLU
Chi-restraints excluded: chain C residue  591 THR
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain C residue  669 GLU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  848 ILE
Chi-restraints excluded: chain D residue  888 THR
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 165 optimal weight:   10.0000
   chunk 36 optimal weight:    0.2980
   chunk 107 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 183 optimal weight:    1.9990
   chunk 152 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 96 optimal weight:    0.6980
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 588 HIS
C 145 GLN
** C 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.3849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  16044  Z= 0.248
  Angle     :  0.605   8.785  21814  Z= 0.318
  Chirality :  0.048   0.225   2380
  Planarity :  0.004   0.040   2780
  Dihedral  :  6.045  58.499   2184
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 18.86 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.53 (0.19), residues: 1922
  helix:  0.46 (0.30), residues: 302
  sheet:  0.02 (0.23), residues: 478
  loop : -0.72 (0.19), residues: 1142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 152 
 HIS   0.003   0.001   HIS A 460 
 PHE   0.012   0.002   PHE D 788 
 TYR   0.014   0.002   TYR C 639 
 ARG   0.004   0.000   ARG A 615 

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 137
  time to evaluate  : 1.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7404 (mtp85)
REVERT: A  108 MET cc_start: 0.6502 (mpp) cc_final: 0.6032 (mmt)
REVERT: A  109 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7402 (ptp-170)
REVERT: A  135 TYR cc_start: 0.8313 (m-80) cc_final: 0.7955 (m-80)
REVERT: A  446 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7773 (mt)
REVERT: A  583 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6867 (tp30)
REVERT: B  859 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6515 (mp0)
REVERT: C   85 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7432 (mtp85)
REVERT: C  108 MET cc_start: 0.6544 (mpp) cc_final: 0.6002 (mmt)
REVERT: C  135 TYR cc_start: 0.8309 (m-80) cc_final: 0.7973 (m-80)
REVERT: C  427 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7204 (tt0)
REVERT: C  446 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.7837 (mt)
REVERT: C  583 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7337 (tt0)
REVERT: C  615 ARG cc_start: 0.7237 (mtt-85) cc_final: 0.7017 (mtt-85)
REVERT: C  669 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6806 (mm-30)
REVERT: D  859 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6504 (mp0)
  outliers start: 75
  outliers final: 35
  residues processed: 193
  average time/residue: 1.3071
  time to fit residues: 281.1969
Evaluate side-chains
  169 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 125
  time to evaluate  : 1.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  583 GLU
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  848 ILE
Chi-restraints excluded: chain B residue  888 THR
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   85 ARG
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  427 GLU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  531 LEU
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  583 GLU
Chi-restraints excluded: chain C residue  591 THR
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain C residue  669 GLU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  848 ILE
Chi-restraints excluded: chain D residue  888 THR
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 177 optimal weight:    8.9990
   chunk 20 optimal weight:    4.9990
   chunk 104 optimal weight:    0.5980
   chunk 134 optimal weight:    8.9990
   chunk 154 optimal weight:    3.9990
   chunk 102 optimal weight:    4.9990
   chunk 183 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9990
   chunk 111 optimal weight:    0.6980
   chunk 84 optimal weight:    5.9990
   chunk 113 optimal weight:    3.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 145 GLN
A 588 HIS
C 145 GLN
** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 588 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.3923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  16044  Z= 0.275
  Angle     :  0.620   8.635  21814  Z= 0.324
  Chirality :  0.048   0.209   2380
  Planarity :  0.004   0.039   2780
  Dihedral  :  6.063  58.659   2184
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 18.45 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.19), residues: 1922
  helix:  0.53 (0.30), residues: 306
  sheet:  0.02 (0.23), residues: 474
  loop : -0.75 (0.19), residues: 1142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 152 
 HIS   0.004   0.001   HIS A 460 
 PHE   0.011   0.002   PHE B 788 
 TYR   0.015   0.002   TYR A 639 
 ARG   0.004   0.000   ARG A 615 

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 129
  time to evaluate  : 1.934 
Fit side-chains
REVERT: A  108 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.6000 (mmt)
REVERT: A  109 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7426 (ptp-170)
REVERT: A  446 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.7800 (mt)
REVERT: A  583 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6961 (tp30)
REVERT: B  859 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6517 (mp0)
REVERT: B  873 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7120 (mtm-85)
REVERT: C  108 MET cc_start: 0.6598 (mpp) cc_final: 0.6041 (mmt)
REVERT: C  355 ASN cc_start: 0.8016 (m-40) cc_final: 0.7769 (m-40)
REVERT: C  427 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7216 (tt0)
REVERT: C  446 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7825 (mt)
REVERT: C  669 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6848 (mm-30)
REVERT: D  859 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6507 (mp0)
  outliers start: 85
  outliers final: 35
  residues processed: 192
  average time/residue: 1.3526
  time to fit residues: 288.2023
Evaluate side-chains
  169 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 126
  time to evaluate  : 1.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  583 GLU
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  848 ILE
Chi-restraints excluded: chain B residue  873 ARG
Chi-restraints excluded: chain B residue  888 THR
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  316 GLU
Chi-restraints excluded: chain C residue  385 LEU
Chi-restraints excluded: chain C residue  427 GLU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  531 LEU
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  591 THR
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain C residue  669 GLU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  848 ILE
Chi-restraints excluded: chain D residue  888 THR
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 109 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 116 optimal weight:    4.9990
   chunk 124 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0870
   chunk 17 optimal weight:    1.9990
   chunk 143 optimal weight:    0.7980
   chunk 166 optimal weight:    1.9990
   chunk 175 optimal weight:    6.9990
   overall best weight:    0.9762

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

Flipped N/Q/H residues before XYZ refinement:
A 145 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.4071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  16044  Z= 0.192
  Angle     :  0.580   9.219  21814  Z= 0.305
  Chirality :  0.047   0.194   2380
  Planarity :  0.004   0.039   2780
  Dihedral  :  5.873  57.896   2184
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 20.45 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.48 (0.19), residues: 1922
  helix:  0.64 (0.30), residues: 306
  sheet:  0.12 (0.23), residues: 472
  loop : -0.77 (0.19), residues: 1144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 152 
 HIS   0.002   0.001   HIS A 460 
 PHE   0.013   0.001   PHE B 788 
 TYR   0.013   0.001   TYR C 639 
 ARG   0.007   0.000   ARG D 934 

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 133
  time to evaluate  : 1.905 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6024 (mmt)
REVERT: A  135 TYR cc_start: 0.8302 (m-80) cc_final: 0.7958 (m-80)
REVERT: A  446 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7820 (mt)
REVERT: B  859 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6511 (mp0)
REVERT: B  873 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7261 (mtm-85)
REVERT: C   85 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7365 (mtp85)
REVERT: C  105 THR cc_start: 0.8366 (p) cc_final: 0.8155 (t)
REVERT: C  108 MET cc_start: 0.6633 (mpp) cc_final: 0.6078 (mmt)
REVERT: C  135 TYR cc_start: 0.8289 (m-80) cc_final: 0.7945 (m-80)
REVERT: C  446 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.7843 (mt)
REVERT: D  859 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6508 (mp0)
  outliers start: 56
  outliers final: 24
  residues processed: 176
  average time/residue: 1.3823
  time to fit residues: 269.9591
Evaluate side-chains
  149 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 1.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  873 ARG
Chi-restraints excluded: chain B residue  888 THR
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   85 ARG
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  888 THR
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 160 optimal weight:    5.9990
   chunk 170 optimal weight:    6.9990
   chunk 175 optimal weight:    0.9990
   chunk 102 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 134 optimal weight:    2.9990
   chunk 52 optimal weight:    8.9990
   chunk 154 optimal weight:    7.9990
   chunk 161 optimal weight:   20.0000
   chunk 112 optimal weight:    7.9990
   chunk 180 optimal weight:    4.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 120 HIS
A 145 GLN
A 422 HIS
C 120 HIS
C 422 HIS
** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.4040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  16044  Z= 0.377
  Angle     :  0.678   9.232  21814  Z= 0.354
  Chirality :  0.050   0.209   2380
  Planarity :  0.005   0.040   2780
  Dihedral  :  6.277  59.720   2184
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.74 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -0.68 (0.19), residues: 1922
  helix:  0.43 (0.30), residues: 306
  sheet: -0.02 (0.23), residues: 468
  loop : -0.88 (0.19), residues: 1148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 152 
 HIS   0.005   0.001   HIS A 460 
 PHE   0.011   0.002   PHE A 310 
 TYR   0.016   0.002   TYR C 234 
 ARG   0.009   0.001   ARG C 364 

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 132
  time to evaluate  : 1.952 
Fit side-chains
REVERT: A  108 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.6032 (mmt)
REVERT: A  355 ASN cc_start: 0.8140 (m-40) cc_final: 0.7912 (m-40)
REVERT: A  446 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7728 (mt)
REVERT: A  583 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6908 (tp30)
REVERT: C  355 ASN cc_start: 0.8145 (m-40) cc_final: 0.7917 (m-40)
REVERT: C  446 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7754 (mt)
REVERT: D  859 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6491 (mp0)
  outliers start: 54
  outliers final: 29
  residues processed: 173
  average time/residue: 1.2717
  time to fit residues: 246.5621
Evaluate side-chains
  158 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 2.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  583 GLU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  888 THR
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  582 LEU
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  888 THR
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 110 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 125 optimal weight:    0.9980
   chunk 189 optimal weight:    1.9990
   chunk 174 optimal weight:    5.9990
   chunk 150 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 116 optimal weight:    3.9990
   chunk 92 optimal weight:    5.9990
   chunk 119 optimal weight:    0.8980
   chunk 160 optimal weight:    5.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 588 HIS
B 831 GLN
C 588 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.4206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  16044  Z= 0.193
  Angle     :  0.585   8.311  21814  Z= 0.308
  Chirality :  0.047   0.298   2380
  Planarity :  0.004   0.042   2780
  Dihedral  :  5.905  58.931   2184
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 21.74 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.56 (0.19), residues: 1922
  helix:  0.64 (0.30), residues: 304
  sheet:  0.05 (0.23), residues: 472
  loop : -0.82 (0.19), residues: 1146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 152 
 HIS   0.004   0.001   HIS C 588 
 PHE   0.014   0.001   PHE B 788 
 TYR   0.014   0.001   TYR C 639 
 ARG   0.009   0.000   ARG C 364 

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 131
  time to evaluate  : 1.865 
Fit side-chains
REVERT: A  108 MET cc_start: 0.6508 (OUTLIER) cc_final: 0.6094 (mmt)
REVERT: A  135 TYR cc_start: 0.8289 (m-80) cc_final: 0.7941 (m-80)
REVERT: A  412 ASP cc_start: 0.6821 (p0) cc_final: 0.6352 (m-30)
REVERT: A  446 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7827 (mt)
REVERT: B  859 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6571 (mp0)
REVERT: C  105 THR cc_start: 0.8394 (p) cc_final: 0.8173 (t)
REVERT: C  108 MET cc_start: 0.6596 (mpp) cc_final: 0.6166 (mmt)
REVERT: C  135 TYR cc_start: 0.8292 (m-80) cc_final: 0.7948 (m-80)
REVERT: C  412 ASP cc_start: 0.6763 (p0) cc_final: 0.6322 (m-30)
REVERT: C  446 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.7854 (mt)
REVERT: D  859 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6519 (mp0)
  outliers start: 39
  outliers final: 27
  residues processed: 161
  average time/residue: 1.2861
  time to fit residues: 231.8647
Evaluate side-chains
  151 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 121
  time to evaluate  : 1.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  888 THR
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  888 THR
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 138 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 150 optimal weight:    0.4980
   chunk 63 optimal weight:    4.9990
   chunk 155 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 132 optimal weight:    0.6980
   chunk 8 optimal weight:    0.1980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.150640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.126661 restraints weight = 17761.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.80
r_work: 0.3393 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.4372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  16044  Z= 0.163
  Angle     :  0.559   8.152  21814  Z= 0.294
  Chirality :  0.047   0.274   2380
  Planarity :  0.004   0.042   2780
  Dihedral  :  5.742  58.748   2184
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 21.92 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.47 (0.19), residues: 1922
  helix:  0.88 (0.31), residues: 302
  sheet:  0.31 (0.24), residues: 442
  loop : -0.90 (0.18), residues: 1178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 152 
 HIS   0.005   0.001   HIS A 588 
 PHE   0.018   0.001   PHE C 587 
 TYR   0.014   0.001   TYR D 832 
 ARG   0.009   0.000   ARG A 364 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5594.62 seconds
wall clock time: 101 minutes 58.61 seconds (6118.61 seconds total)