Starting phenix.real_space_refine
on Tue Jun 10 21:56:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bh7_44535/06_2025/9bh7_44535.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bh7_44535/06_2025/9bh7_44535.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bh7_44535/06_2025/9bh7_44535.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bh7_44535/06_2025/9bh7_44535.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bh7_44535/06_2025/9bh7_44535.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bh7_44535/06_2025/9bh7_44535.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.032
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      80      5.16       5
     C    7776      2.51       5
     N    2112      2.21       5
     O    2198      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12166
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6083
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 772, 6083
          Classifications: {'peptide': 772}
          Link IDs: {'PTRANS': 22, 'TRANS': 749}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 6083
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 772, 6083
          Classifications: {'peptide': 772}
          Link IDs: {'PTRANS': 22, 'TRANS': 749}
          Chain breaks: 5
  Time building chain proxies: 8.19, per 1000 atoms: 0.67
  Number of scatterers: 12166
  At special positions: 0
  Unit cell: (117.453, 150.773, 89.964, 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      80     16.00
     O    2198      8.00
     N    2112      7.00
     C    7776      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.10
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2896

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 9 sheets defined
      63.1% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 74
    Processing helix  chain 'A' and resid 77 through 88
    Processing helix  chain 'A' and resid 93 through 102
    Processing helix  chain 'A' and resid 120 through 136
      removed outlier: 4.360A  pdb=" N   VAL A 124 " --> pdb=" O   GLY A 120 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   ALA A 125 " --> pdb=" O   LYS A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 165
      removed outlier: 3.976A  pdb=" N   GLU A 163 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   VAL A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 204
    Processing helix  chain 'A' and resid 205 through 208
      removed outlier: 4.591A  pdb=" N   ASP A 208 " --> pdb=" O   ASN A 205 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 205 through 208'
    Processing helix  chain 'A' and resid 217 through 223
      removed outlier: 3.896A  pdb=" N   GLY A 222 " --> pdb=" O   HIS A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 247
      removed outlier: 3.508A  pdb=" N   LEU A 229 " --> pdb=" O   HIS A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
    Processing helix  chain 'A' and resid 325 through 335
      removed outlier: 4.363A  pdb=" N   THR A 333 " --> pdb=" O   LEU A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 368
    Processing helix  chain 'A' and resid 383 through 396
    Processing helix  chain 'A' and resid 402 through 412
      removed outlier: 3.691A  pdb=" N   LYS A 407 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
      Proline residue:  A 410  - end of helix
    Processing helix  chain 'A' and resid 421 through 435
    Processing helix  chain 'A' and resid 444 through 449
      removed outlier: 3.806A  pdb=" N   SER A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 479
    Processing helix  chain 'A' and resid 500 through 510
    Processing helix  chain 'A' and resid 528 through 542
    Processing helix  chain 'A' and resid 546 through 557
    Processing helix  chain 'A' and resid 557 through 564
    Processing helix  chain 'A' and resid 578 through 592
    Processing helix  chain 'A' and resid 612 through 622
    Processing helix  chain 'A' and resid 624 through 640
      removed outlier: 3.990A  pdb=" N   ASP A 630 " --> pdb=" O   ALA A 626 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LYS A 640 " --> pdb=" O   GLN A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 655
    Processing helix  chain 'A' and resid 665 through 676
      removed outlier: 3.522A  pdb=" N   LYS A 675 " --> pdb=" O   CYS A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 688
    Processing helix  chain 'A' and resid 690 through 700
      removed outlier: 4.172A  pdb=" N   ARG A 696 " --> pdb=" O   GLY A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 729
    Processing helix  chain 'A' and resid 733 through 742
    Processing helix  chain 'A' and resid 744 through 770
    Processing helix  chain 'A' and resid 771 through 780
      removed outlier: 4.220A  pdb=" N   GLN A 780 " --> pdb=" O   LEU A 776 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 788
    Processing helix  chain 'A' and resid 790 through 794
      removed outlier: 3.508A  pdb=" N   CYS A 794 " --> pdb=" O   ARG A 791 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 795 through 799
    Processing helix  chain 'A' and resid 803 through 814
    Processing helix  chain 'A' and resid 817 through 824
    Processing helix  chain 'A' and resid 825 through 835
    Processing helix  chain 'A' and resid 871 through 892
    Processing helix  chain 'B' and resid 70 through 75
      removed outlier: 3.619A  pdb=" N   TRP B  74 " --> pdb=" O   LEU B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 87
      removed outlier: 3.683A  pdb=" N   LYS B  83 " --> pdb=" O   ALA B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 102
    Processing helix  chain 'B' and resid 120 through 136
      removed outlier: 4.155A  pdb=" N   VAL B 124 " --> pdb=" O   GLY B 120 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   ALA B 125 " --> pdb=" O   LYS B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 162
    Processing helix  chain 'B' and resid 163 through 165
      No H-bonds generated for 'chain 'B' and resid 163 through 165'
    Processing helix  chain 'B' and resid 180 through 184
    Processing helix  chain 'B' and resid 191 through 204
    Processing helix  chain 'B' and resid 206 through 208
      No H-bonds generated for 'chain 'B' and resid 206 through 208'
    Processing helix  chain 'B' and resid 219 through 224
      removed outlier: 4.308A  pdb=" N   ASP B 223 " --> pdb=" O   HIS B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 247
      removed outlier: 3.535A  pdb=" N   GLU B 231 " --> pdb=" O   GLY B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 278
    Processing helix  chain 'B' and resid 325 through 335
      removed outlier: 4.562A  pdb=" N   THR B 333 " --> pdb=" O   LEU B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 368
    Processing helix  chain 'B' and resid 383 through 396
      removed outlier: 3.923A  pdb=" N   LEU B 387 " --> pdb=" O   GLU B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 409
      removed outlier: 3.610A  pdb=" N   LYS B 407 " --> pdb=" O   SER B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 435
    Processing helix  chain 'B' and resid 443 through 450
      removed outlier: 4.324A  pdb=" N   SER B 447 " --> pdb=" O   THR B 443 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   SER B 448 " --> pdb=" O   SER B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 479
    Processing helix  chain 'B' and resid 500 through 510
    Processing helix  chain 'B' and resid 528 through 542
    Processing helix  chain 'B' and resid 546 through 557
    Processing helix  chain 'B' and resid 557 through 564
    Processing helix  chain 'B' and resid 578 through 592
    Processing helix  chain 'B' and resid 612 through 622
    Processing helix  chain 'B' and resid 624 through 640
      removed outlier: 4.010A  pdb=" N   ASP B 630 " --> pdb=" O   ALA B 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 647 through 655
    Processing helix  chain 'B' and resid 665 through 676
      removed outlier: 3.527A  pdb=" N   LYS B 675 " --> pdb=" O   CYS B 671 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 688
    Processing helix  chain 'B' and resid 690 through 700
    Processing helix  chain 'B' and resid 706 through 730
    Processing helix  chain 'B' and resid 733 through 742
    Processing helix  chain 'B' and resid 744 through 770
    Processing helix  chain 'B' and resid 771 through 788
      removed outlier: 3.613A  pdb=" N   LEU B 776 " --> pdb=" O   HIS B 772 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   GLN B 780 " --> pdb=" O   LEU B 776 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   PHE B 781 " --> pdb=" O   LEU B 777 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLN B 782 " --> pdb=" O   LEU B 778 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LYS B 783 " --> pdb=" O   SER B 779 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 790 through 796
      removed outlier: 4.161A  pdb=" N   ASP B 795 " --> pdb=" O   GLU B 792 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 814
    Processing helix  chain 'B' and resid 817 through 824
    Processing helix  chain 'B' and resid 825 through 836
    Processing helix  chain 'B' and resid 871 through 892
    Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171
      removed outlier: 6.645A  pdb=" N   ALA A 140 " --> pdb=" O   ALA A 187 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   CYS A 189 " --> pdb=" O   ALA A 140 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   PHE A 142 " --> pdb=" O   CYS A 189 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LYS A 139 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   VAL A 213 " --> pdb=" O   LYS A 139 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LEU A 141 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   VAL A 215 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ILE A 143 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 293
    Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 293
      removed outlier: 6.504A  pdb=" N   VAL A 457 " --> pdb=" O   ILE A 493 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   ILE A 495 " --> pdb=" O   VAL A 457 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ILE A 459 " --> pdb=" O   ILE A 495 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   LEU A 341 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   VAL A 340 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   ALA A 442 " --> pdb=" O   VAL A 340 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   LEU A 342 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   ALA A 414 " --> pdb=" O   ALA A 441 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 464
    Processing sheet with id=AA5, first strand: chain 'A' and resid 595 through 598
    Processing sheet with id=AA6, first strand: chain 'B' and resid 168 through 171
      removed outlier: 6.702A  pdb=" N   ALA B 140 " --> pdb=" O   ALA B 187 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   CYS B 189 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   PHE B 142 " --> pdb=" O   CYS B 189 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   LYS B 139 " --> pdb=" O   GLY B 211 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   VAL B 213 " --> pdb=" O   LYS B 139 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   LEU B 141 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 5.551A  pdb=" N   VAL B 215 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ILE B 143 " --> pdb=" O   VAL B 215 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   GLY B 211 " --> pdb=" O   GLN B 260 " (cutoff:3.500A)
      removed outlier: 8.205A  pdb=" N   VAL B 262 " --> pdb=" O   GLY B 211 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   VAL B 213 " --> pdb=" O   VAL B 262 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   MET B 264 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   VAL B 215 " --> pdb=" O   MET B 264 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 309 through 312
      removed outlier: 7.216A  pdb=" N   ILE B 302 " --> pdb=" O   VAL B 310 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   VAL B 457 " --> pdb=" O   ILE B 493 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   ILE B 495 " --> pdb=" O   VAL B 457 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ILE B 459 " --> pdb=" O   ILE B 495 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   VAL B 340 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   ALA B 442 " --> pdb=" O   VAL B 340 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   LEU B 342 " --> pdb=" O   ALA B 442 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ALA B 414 " --> pdb=" O   ALA B 441 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 463 through 464
    Processing sheet with id=AA9, first strand: chain 'B' and resid 595 through 598

    698 hydrogen bonds defined for protein.
    2025 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.39

  Time building geometry restraints manager: 3.51 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3976
        1.34 -     1.46: 2107
        1.46 -     1.58: 6165
        1.58 -     1.69: 0
        1.69 -     1.81: 126
  Bond restraints: 12374
  Sorted by residual:
  bond pdb=" CB  CYS B 496 "
       pdb=" SG  CYS B 496 "
    ideal  model  delta    sigma   weight residual
    1.808  1.770  0.038 3.30e-02 9.18e+02 1.35e+00
  bond pdb=" CB  CYS A 496 "
       pdb=" SG  CYS A 496 "
    ideal  model  delta    sigma   weight residual
    1.808  1.772  0.036 3.30e-02 9.18e+02 1.17e+00
  bond pdb=" CA  VAL A 797 "
       pdb=" CB  VAL A 797 "
    ideal  model  delta    sigma   weight residual
    1.540  1.552 -0.012 1.36e-02 5.41e+03 7.40e-01
  bond pdb=" CB  VAL A 340 "
       pdb=" CG2 VAL A 340 "
    ideal  model  delta    sigma   weight residual
    1.521  1.494  0.027 3.30e-02 9.18e+02 6.91e-01
  bond pdb=" CG  LEU A 778 "
       pdb=" CD2 LEU A 778 "
    ideal  model  delta    sigma   weight residual
    1.521  1.494  0.027 3.30e-02 9.18e+02 6.49e-01
  ... (remaining 12369 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 15834
        1.28 -     2.56: 736
        2.56 -     3.84: 117
        3.84 -     5.11: 16
        5.11 -     6.39: 5
  Bond angle restraints: 16708
  Sorted by residual:
  angle pdb=" N   PHE B 781 "
        pdb=" CA  PHE B 781 "
        pdb=" C   PHE B 781 "
      ideal   model   delta    sigma   weight residual
     111.71  115.49   -3.78 1.15e+00 7.56e-01 1.08e+01
  angle pdb=" N   PHE A 781 "
        pdb=" CA  PHE A 781 "
        pdb=" C   PHE A 781 "
      ideal   model   delta    sigma   weight residual
     112.54  116.32   -3.78 1.22e+00 6.72e-01 9.59e+00
  angle pdb=" N   THR A 408 "
        pdb=" CA  THR A 408 "
        pdb=" C   THR A 408 "
      ideal   model   delta    sigma   weight residual
     111.36  114.45   -3.09 1.09e+00 8.42e-01 8.05e+00
  angle pdb=" CB  ARG A 460 "
        pdb=" CG  ARG A 460 "
        pdb=" CD  ARG A 460 "
      ideal   model   delta    sigma   weight residual
     111.30  117.69   -6.39 2.30e+00 1.89e-01 7.73e+00
  angle pdb=" CA  ARG A 460 "
        pdb=" CB  ARG A 460 "
        pdb=" CG  ARG A 460 "
      ideal   model   delta    sigma   weight residual
     114.10  108.59    5.51 2.00e+00 2.50e-01 7.59e+00
  ... (remaining 16703 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 6997
       17.73 -    35.45: 416
       35.45 -    53.18: 56
       53.18 -    70.91: 26
       70.91 -    88.63: 9
  Dihedral angle restraints: 7504
    sinusoidal: 3038
      harmonic: 4466
  Sorted by residual:
  dihedral pdb=" CA  LEU A 101 "
           pdb=" C   LEU A 101 "
           pdb=" N   LEU A 102 "
           pdb=" CA  LEU A 102 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.98  -28.02     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  THR B 662 "
           pdb=" C   THR B 662 "
           pdb=" N   THR B 663 "
           pdb=" CA  THR B 663 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.46   27.54     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  ARG B 311 "
           pdb=" C   ARG B 311 "
           pdb=" N   GLU B 312 "
           pdb=" CA  GLU B 312 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.85   27.15     0      5.00e+00 4.00e-02 2.95e+01
  ... (remaining 7501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1158
       0.033 -    0.066: 551
       0.066 -    0.099: 153
       0.099 -    0.132: 73
       0.132 -    0.165: 13
  Chirality restraints: 1948
  Sorted by residual:
  chirality pdb=" CA  VAL A 409 "
            pdb=" N   VAL A 409 "
            pdb=" C   VAL A 409 "
            pdb=" CB  VAL A 409 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.28    0.17 2.00e-01 2.50e+01 6.81e-01
  chirality pdb=" CA  LYS B 206 "
            pdb=" N   LYS B 206 "
            pdb=" C   LYS B 206 "
            pdb=" CB  LYS B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.11e-01
  chirality pdb=" CA  ILE A 459 "
            pdb=" N   ILE A 459 "
            pdb=" C   ILE A 459 "
            pdb=" CB  ILE A 459 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.96e-01
  ... (remaining 1945 not shown)

  Planarity restraints: 2096
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 758 "    0.012 2.00e-02 2.50e+03   1.74e-02 6.04e+00
        pdb=" CG  TYR A 758 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 758 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 758 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 758 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 758 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 758 "   -0.024 2.00e-02 2.50e+03
        pdb=" OH  TYR A 758 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 784 "    0.190 9.50e-02 1.11e+02   8.57e-02 5.13e+00
        pdb=" NE  ARG B 784 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 784 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 784 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 784 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 745 "    0.160 9.50e-02 1.11e+02   7.26e-02 4.32e+00
        pdb=" NE  ARG B 745 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 745 "    0.017 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 745 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 745 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 2093 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 4169
        2.88 -     3.38: 12043
        3.38 -     3.89: 19128
        3.89 -     4.39: 22610
        4.39 -     4.90: 38202
  Nonbonded interactions: 96152
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 317 "
            pdb=" OG  SER B 328 "
     model   vdw
     2.370 3.040
  nonbonded pdb=" NZ  LYS B 121 "
            pdb=" O   SER B 265 "
     model   vdw
     2.387 3.120
  nonbonded pdb=" OH  TYR B  84 "
            pdb=" OE1 GLU B 126 "
     model   vdw
     2.404 3.040
  nonbonded pdb=" OD1 ASN B 337 "
            pdb=" NH2 ARG B 438 "
     model   vdw
     2.405 3.120
  nonbonded pdb=" NZ  LYS A  83 "
            pdb=" OE1 GLU A 163 "
     model   vdw
     2.409 3.120
  ... (remaining 96147 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.940
  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:          0.520
  Check model and map are aligned:         0.080
  Set scattering table:                    0.130
  Process input model:                     30.890
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12374  Z= 0.136
  Angle     :  0.635   6.393  16708  Z= 0.389
  Chirality :  0.045   0.165   1948
  Planarity :  0.007   0.086   2096
  Dihedral  : 12.657  88.633   4608
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  0.66 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.19), residues: 1520
  helix: -0.99 (0.14), residues: 868
  sheet:  0.36 (0.38), residues: 158
  loop : -0.33 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 863 
 HIS   0.006   0.001   HIS B 710 
 PHE   0.015   0.002   PHE B 632 
 TYR   0.026   0.004   TYR A 758 
 ARG   0.019   0.003   ARG B 745 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19666 (  696)
  hydrogen bonds       : angle       7.39186 ( 2025)
  covalent geometry    : bond        0.00297 (12374)
  covalent geometry    : angle       0.63539 (16708)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 313
  time to evaluate  : 1.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6345 (mt-10)
REVERT: A  151 LYS cc_start: 0.8708 (mttt) cc_final: 0.8407 (mttp)
REVERT: A  557 THR cc_start: 0.8053 (m) cc_final: 0.7692 (p)
REVERT: B  126 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6505 (mt-10)
REVERT: B  151 LYS cc_start: 0.8800 (mttt) cc_final: 0.8511 (mttp)
REVERT: B  531 MET cc_start: 0.7282 (tpp) cc_final: 0.7028 (tpt)
REVERT: B  802 LEU cc_start: 0.8595 (tp) cc_final: 0.8372 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 313
  average time/residue: 0.3228
  time to fit residues: 133.2026
Evaluate side-chains
  172 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 130 optimal weight:    0.9990
   chunk 116 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 62 optimal weight:    0.6980
   chunk 120 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0060
   chunk 73 optimal weight:    0.0980
   chunk 89 optimal weight:    0.9980
   chunk 139 optimal weight:    1.9990
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
A 110 ASN
A 416 HIS
A 434 GLN
A 592 ASN
A 716 HIS
B 110 ASN
B 219 HIS
B 416 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.123675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.100724 restraints weight = 22150.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.102773 restraints weight = 17492.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.104057 restraints weight = 12814.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12374  Z= 0.135
  Angle     :  0.592  10.379  16708  Z= 0.318
  Chirality :  0.041   0.138   1948
  Planarity :  0.004   0.043   2096
  Dihedral  :  5.299  20.150   1662
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  :  6.37 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.21), residues: 1520
  helix:  0.77 (0.16), residues: 890
  sheet:  0.52 (0.39), residues: 160
  loop :  0.44 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  95 
 HIS   0.009   0.001   HIS A  85 
 PHE   0.023   0.002   PHE A 313 
 TYR   0.024   0.002   TYR A 228 
 ARG   0.005   0.001   ARG B 784 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04535 (  696)
  hydrogen bonds       : angle       4.89350 ( 2025)
  covalent geometry    : bond        0.00295 (12374)
  covalent geometry    : angle       0.59238 (16708)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 197
  time to evaluate  : 1.454 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8671 (tt)
REVERT: A  151 LYS cc_start: 0.8565 (mttt) cc_final: 0.8312 (mttp)
REVERT: A  154 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8179 (ttmm)
REVERT: A  167 LYS cc_start: 0.7907 (tppt) cc_final: 0.7536 (mmtm)
REVERT: A  331 TYR cc_start: 0.6833 (t80) cc_final: 0.6519 (t80)
REVERT: A  587 MET cc_start: 0.8238 (tpp) cc_final: 0.7857 (tpp)
REVERT: A  667 TYR cc_start: 0.8168 (t80) cc_final: 0.7960 (t80)
REVERT: B  151 LYS cc_start: 0.8685 (mttt) cc_final: 0.8464 (mttp)
REVERT: B  154 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8415 (ttmm)
  outliers start: 36
  outliers final: 16
  residues processed: 213
  average time/residue: 0.2720
  time to fit residues: 81.5710
Evaluate side-chains
  178 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 1.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  154 LYS
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  518 CYS
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  886 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   84 TYR
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  886 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 29 optimal weight:    0.0980
   chunk 113 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 112 optimal weight:    0.9980
   chunk 153 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 127 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0470
   overall best weight:    1.0080

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

Flipped N/Q/H residues before XYZ refinement:
A  73 ASN
A 325 HIS
B 716 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.121751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.099249 restraints weight = 22248.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.102381 restraints weight = 20947.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.103111 restraints weight = 16438.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12374  Z= 0.152
  Angle     :  0.557   9.274  16708  Z= 0.295
  Chirality :  0.040   0.133   1948
  Planarity :  0.004   0.041   2096
  Dihedral  :  4.825  16.921   1662
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 10.19 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.21), residues: 1520
  helix:  1.22 (0.17), residues: 874
  sheet:  0.34 (0.38), residues: 166
  loop :  0.62 (0.30), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 863 
 HIS   0.006   0.001   HIS A 416 
 PHE   0.021   0.002   PHE A 313 
 TYR   0.018   0.002   TYR A 228 
 ARG   0.005   0.000   ARG A 823 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04213 (  696)
  hydrogen bonds       : angle       4.62051 ( 2025)
  covalent geometry    : bond        0.00350 (12374)
  covalent geometry    : angle       0.55732 (16708)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 183
  time to evaluate  : 1.430 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8728 (tt)
REVERT: A  151 LYS cc_start: 0.8494 (mttt) cc_final: 0.8233 (mttp)
REVERT: A  154 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8252 (ttmt)
REVERT: A  166 ILE cc_start: 0.8141 (mm) cc_final: 0.7716 (mt)
REVERT: A  167 LYS cc_start: 0.8051 (tppt) cc_final: 0.7737 (mmtm)
REVERT: B  130 LEU cc_start: 0.9082 (tp) cc_final: 0.8815 (tp)
REVERT: B  151 LYS cc_start: 0.8523 (mttt) cc_final: 0.8283 (mttm)
REVERT: B  172 MET cc_start: 0.7786 (mtt) cc_final: 0.7529 (mtt)
REVERT: B  316 MET cc_start: 0.7089 (ttp) cc_final: 0.6720 (mmt)
  outliers start: 30
  outliers final: 21
  residues processed: 199
  average time/residue: 0.2726
  time to fit residues: 78.5099
Evaluate side-chains
  183 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 160
  time to evaluate  : 1.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  154 LYS
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  189 CYS
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  355 ASP
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  861 THR
Chi-restraints excluded: chain B residue  886 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 106 optimal weight:    5.9990
   chunk 14 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 76 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 132 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.122591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.099521 restraints weight = 22120.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.103312 restraints weight = 21045.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.103668 restraints weight = 16553.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.3748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12374  Z= 0.129
  Angle     :  0.523   8.692  16708  Z= 0.277
  Chirality :  0.039   0.131   1948
  Planarity :  0.003   0.038   2096
  Dihedral  :  4.521  17.780   1662
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 11.39 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.21), residues: 1520
  helix:  1.51 (0.17), residues: 874
  sheet:  0.39 (0.38), residues: 166
  loop :  0.59 (0.30), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  95 
 HIS   0.004   0.001   HIS B 710 
 PHE   0.021   0.001   PHE A 313 
 TYR   0.021   0.002   TYR B 667 
 ARG   0.005   0.000   ARG B 823 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03753 (  696)
  hydrogen bonds       : angle       4.46532 ( 2025)
  covalent geometry    : bond        0.00298 (12374)
  covalent geometry    : angle       0.52322 (16708)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 174
  time to evaluate  : 1.378 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8730 (tt)
REVERT: A  151 LYS cc_start: 0.8393 (mttt) cc_final: 0.8039 (mttp)
REVERT: A  167 LYS cc_start: 0.8146 (tppt) cc_final: 0.7851 (mmtm)
REVERT: A  649 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.6908 (t-170)
REVERT: B  130 LEU cc_start: 0.9130 (tp) cc_final: 0.8794 (tp)
REVERT: B  151 LYS cc_start: 0.8453 (mttt) cc_final: 0.8170 (mttp)
REVERT: B  172 MET cc_start: 0.7823 (mtt) cc_final: 0.7521 (mtt)
REVERT: B  426 ASP cc_start: 0.7895 (t0) cc_final: 0.7588 (t0)
REVERT: B  587 MET cc_start: 0.8310 (tpp) cc_final: 0.7966 (tpp)
REVERT: B  649 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.6975 (t-170)
  outliers start: 33
  outliers final: 21
  residues processed: 192
  average time/residue: 0.2459
  time to fit residues: 67.8344
Evaluate side-chains
  180 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  582 ILE
Chi-restraints excluded: chain A residue  649 HIS
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain B residue  355 ASP
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  649 HIS
Chi-restraints excluded: chain B residue  878 LEU
Chi-restraints excluded: chain B residue  886 ILE
Chi-restraints excluded: chain B residue  887 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 91 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 76 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 97 optimal weight:    3.9990
   chunk 115 optimal weight:    0.4980
   chunk 54 optimal weight:    0.2980
   chunk 26 optimal weight:    2.9990
   chunk 136 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.6982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.122241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.099290 restraints weight = 22032.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.103423 restraints weight = 18815.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.103338 restraints weight = 15571.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.3977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12374  Z= 0.122
  Angle     :  0.512   7.752  16708  Z= 0.269
  Chirality :  0.039   0.127   1948
  Planarity :  0.003   0.038   2096
  Dihedral  :  4.317  16.761   1662
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 12.29 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.21), residues: 1520
  helix:  1.68 (0.17), residues: 874
  sheet:  0.53 (0.39), residues: 156
  loop :  0.55 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  95 
 HIS   0.005   0.001   HIS B 710 
 PHE   0.020   0.001   PHE A 313 
 TYR   0.018   0.002   TYR B 667 
 ARG   0.005   0.000   ARG B 823 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03613 (  696)
  hydrogen bonds       : angle       4.31622 ( 2025)
  covalent geometry    : bond        0.00277 (12374)
  covalent geometry    : angle       0.51244 (16708)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 179
  time to evaluate  : 1.426 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.8598 (mttt) cc_final: 0.8352 (mttm)
REVERT: A  167 LYS cc_start: 0.8227 (tppt) cc_final: 0.7946 (mmtm)
REVERT: A  189 CYS cc_start: 0.8203 (p) cc_final: 0.7942 (p)
REVERT: A  220 MET cc_start: 0.8341 (mmm) cc_final: 0.8000 (mtp)
REVERT: A  316 MET cc_start: 0.6583 (ttt) cc_final: 0.6089 (mmt)
REVERT: A  587 MET cc_start: 0.8200 (tpp) cc_final: 0.7849 (tpp)
REVERT: A  649 HIS cc_start: 0.8402 (OUTLIER) cc_final: 0.7019 (t-170)
REVERT: A  874 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7413 (pt0)
REVERT: B  151 LYS cc_start: 0.8482 (mttt) cc_final: 0.8196 (mttp)
REVERT: B  172 MET cc_start: 0.7851 (mtt) cc_final: 0.7541 (mtt)
REVERT: B  587 MET cc_start: 0.8284 (tpp) cc_final: 0.7943 (tpp)
REVERT: B  649 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.6868 (t-170)
  outliers start: 37
  outliers final: 25
  residues processed: 199
  average time/residue: 0.2685
  time to fit residues: 76.0612
Evaluate side-chains
  190 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 1.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  549 ASP
Chi-restraints excluded: chain A residue  649 HIS
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain A residue  886 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  189 CYS
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain B residue  355 ASP
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  582 ILE
Chi-restraints excluded: chain B residue  649 HIS
Chi-restraints excluded: chain B residue  886 ILE
Chi-restraints excluded: chain B residue  887 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 112 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 103 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 106 optimal weight:    0.1980
   chunk 101 optimal weight:    8.9990
   chunk 149 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0170
   chunk 129 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
B 158 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.122860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.100147 restraints weight = 22217.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.103451 restraints weight = 19512.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.103900 restraints weight = 14413.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.4143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12374  Z= 0.110
  Angle     :  0.504   7.702  16708  Z= 0.262
  Chirality :  0.038   0.127   1948
  Planarity :  0.003   0.039   2096
  Dihedral  :  4.166  16.432   1662
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 13.94 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.22), residues: 1520
  helix:  1.91 (0.17), residues: 866
  sheet:  0.59 (0.39), residues: 156
  loop :  0.54 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 863 
 HIS   0.005   0.001   HIS B 416 
 PHE   0.015   0.001   PHE B 161 
 TYR   0.017   0.002   TYR B 667 
 ARG   0.005   0.000   ARG B 823 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03447 (  696)
  hydrogen bonds       : angle       4.19652 ( 2025)
  covalent geometry    : bond        0.00248 (12374)
  covalent geometry    : angle       0.50418 (16708)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 171
  time to evaluate  : 1.429 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 CYS cc_start: 0.8128 (p) cc_final: 0.7917 (p)
REVERT: A  190 THR cc_start: 0.7595 (OUTLIER) cc_final: 0.7205 (m)
REVERT: A  220 MET cc_start: 0.8266 (mmm) cc_final: 0.8056 (mtp)
REVERT: A  316 MET cc_start: 0.6618 (ttt) cc_final: 0.5932 (mmt)
REVERT: A  587 MET cc_start: 0.8195 (tpp) cc_final: 0.7859 (tpp)
REVERT: A  649 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.6995 (t-170)
REVERT: A  874 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7456 (pt0)
REVERT: A  885 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7871 (tmm)
REVERT: B  151 LYS cc_start: 0.8466 (mttt) cc_final: 0.8173 (mttp)
REVERT: B  172 MET cc_start: 0.7807 (mtt) cc_final: 0.7498 (mtt)
REVERT: B  347 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7914 (mtmt)
REVERT: B  587 MET cc_start: 0.8288 (tpp) cc_final: 0.7964 (tpp)
REVERT: B  649 HIS cc_start: 0.8441 (OUTLIER) cc_final: 0.6892 (t-170)
  outliers start: 36
  outliers final: 24
  residues processed: 188
  average time/residue: 0.2553
  time to fit residues: 68.2816
Evaluate side-chains
  184 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  649 HIS
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain A residue  885 MET
Chi-restraints excluded: chain A residue  886 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain B residue  355 ASP
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  582 ILE
Chi-restraints excluded: chain B residue  649 HIS
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain B residue  878 LEU
Chi-restraints excluded: chain B residue  886 ILE
Chi-restraints excluded: chain B residue  887 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 104 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 140 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 2 optimal weight:    7.9990
   chunk 63 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.121594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.099208 restraints weight = 22141.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.102994 restraints weight = 19629.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.103108 restraints weight = 16510.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.4230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12374  Z= 0.127
  Angle     :  0.519   7.821  16708  Z= 0.269
  Chirality :  0.039   0.135   1948
  Planarity :  0.003   0.039   2096
  Dihedral  :  4.139  16.587   1662
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 14.17 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.22), residues: 1520
  helix:  1.91 (0.17), residues: 868
  sheet:  0.53 (0.39), residues: 156
  loop :  0.49 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 863 
 HIS   0.005   0.001   HIS B 710 
 PHE   0.013   0.001   PHE A 765 
 TYR   0.016   0.002   TYR B 667 
 ARG   0.006   0.000   ARG A 823 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03502 (  696)
  hydrogen bonds       : angle       4.17120 ( 2025)
  covalent geometry    : bond        0.00294 (12374)
  covalent geometry    : angle       0.51903 (16708)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 168
  time to evaluate  : 1.456 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 THR cc_start: 0.7577 (OUTLIER) cc_final: 0.7204 (m)
REVERT: A  316 MET cc_start: 0.6447 (ttt) cc_final: 0.5949 (mmt)
REVERT: A  587 MET cc_start: 0.8205 (tpp) cc_final: 0.7874 (tpp)
REVERT: A  649 HIS cc_start: 0.8247 (OUTLIER) cc_final: 0.6823 (t-170)
REVERT: A  660 ASP cc_start: 0.7501 (t70) cc_final: 0.7261 (t70)
REVERT: A  696 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8324 (ttp80)
REVERT: A  885 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7849 (tmm)
REVERT: B  151 LYS cc_start: 0.8507 (mttt) cc_final: 0.8214 (mttp)
REVERT: B  172 MET cc_start: 0.7874 (mtt) cc_final: 0.7626 (mtt)
REVERT: B  347 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7906 (mtmt)
REVERT: B  587 MET cc_start: 0.8298 (tpp) cc_final: 0.7988 (tpp)
REVERT: B  649 HIS cc_start: 0.8417 (OUTLIER) cc_final: 0.6851 (t-170)
  outliers start: 40
  outliers final: 29
  residues processed: 188
  average time/residue: 0.2467
  time to fit residues: 66.9541
Evaluate side-chains
  194 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 160
  time to evaluate  : 1.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  172 MET
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  366 HIS
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  649 HIS
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain A residue  885 MET
Chi-restraints excluded: chain A residue  886 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain B residue  355 ASP
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  582 ILE
Chi-restraints excluded: chain B residue  649 HIS
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain B residue  878 LEU
Chi-restraints excluded: chain B residue  886 ILE
Chi-restraints excluded: chain B residue  887 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 141 optimal weight:    2.9990
   chunk 132 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 136 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0070
   overall best weight:    0.6800

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.122082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.099614 restraints weight = 22340.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.104158 restraints weight = 19750.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.104365 restraints weight = 14150.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.4322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12374  Z= 0.118
  Angle     :  0.509   7.318  16708  Z= 0.267
  Chirality :  0.038   0.164   1948
  Planarity :  0.003   0.039   2096
  Dihedral  :  4.090  18.040   1662
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.14 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.22), residues: 1520
  helix:  2.00 (0.17), residues: 866
  sheet:  0.51 (0.39), residues: 156
  loop :  0.40 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 863 
 HIS   0.005   0.001   HIS A  85 
 PHE   0.021   0.001   PHE A 815 
 TYR   0.015   0.001   TYR B 667 
 ARG   0.008   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03420 (  696)
  hydrogen bonds       : angle       4.17046 ( 2025)
  covalent geometry    : bond        0.00269 (12374)
  covalent geometry    : angle       0.50948 (16708)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 162
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 MET cc_start: 0.8190 (tpp) cc_final: 0.7874 (tpp)
REVERT: A  649 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.6811 (t-170)
REVERT: A  660 ASP cc_start: 0.7462 (t70) cc_final: 0.7205 (t70)
REVERT: A  696 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8289 (ttp80)
REVERT: A  885 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7851 (tmm)
REVERT: B  172 MET cc_start: 0.7892 (mtt) cc_final: 0.7656 (mtt)
REVERT: B  347 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7895 (mtmt)
REVERT: B  587 MET cc_start: 0.8272 (tpp) cc_final: 0.7976 (tpp)
REVERT: B  649 HIS cc_start: 0.8345 (OUTLIER) cc_final: 0.5706 (t-170)
  outliers start: 34
  outliers final: 27
  residues processed: 178
  average time/residue: 0.2294
  time to fit residues: 59.5677
Evaluate side-chains
  193 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 162
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  172 MET
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  366 HIS
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  649 HIS
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain A residue  885 MET
Chi-restraints excluded: chain A residue  886 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain B residue  355 ASP
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  582 ILE
Chi-restraints excluded: chain B residue  649 HIS
Chi-restraints excluded: chain B residue  699 LYS
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain B residue  878 LEU
Chi-restraints excluded: chain B residue  886 ILE
Chi-restraints excluded: chain B residue  887 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9980
   chunk 146 optimal weight:    0.0170
   chunk 140 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0050
   chunk 130 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.5632

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.122317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.099902 restraints weight = 22058.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.104392 restraints weight = 18667.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.104735 restraints weight = 12643.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.4429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12374  Z= 0.111
  Angle     :  0.508   8.635  16708  Z= 0.265
  Chirality :  0.038   0.139   1948
  Planarity :  0.003   0.038   2096
  Dihedral  :  4.000  19.067   1662
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.92 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.22), residues: 1520
  helix:  2.08 (0.17), residues: 866
  sheet:  0.52 (0.40), residues: 156
  loop :  0.39 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 863 
 HIS   0.006   0.001   HIS A  85 
 PHE   0.020   0.001   PHE A 313 
 TYR   0.016   0.001   TYR B 667 
 ARG   0.007   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03321 (  696)
  hydrogen bonds       : angle       4.09455 ( 2025)
  covalent geometry    : bond        0.00251 (12374)
  covalent geometry    : angle       0.50751 (16708)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 168
  time to evaluate  : 1.497 
Fit side-chains
   revert: symmetry clash
REVERT: A  220 MET cc_start: 0.8084 (mtp) cc_final: 0.7821 (mtm)
REVERT: A  307 MET cc_start: 0.6248 (tpp) cc_final: 0.6013 (tpp)
REVERT: A  587 MET cc_start: 0.8148 (tpp) cc_final: 0.7837 (tpp)
REVERT: A  649 HIS cc_start: 0.8378 (OUTLIER) cc_final: 0.6939 (t-170)
REVERT: A  660 ASP cc_start: 0.7426 (t70) cc_final: 0.7172 (t70)
REVERT: B  172 MET cc_start: 0.7874 (mtt) cc_final: 0.7609 (mtt)
REVERT: B  426 ASP cc_start: 0.8011 (t0) cc_final: 0.7664 (t0)
REVERT: B  587 MET cc_start: 0.8258 (tpp) cc_final: 0.7960 (tpp)
REVERT: B  649 HIS cc_start: 0.8420 (OUTLIER) cc_final: 0.5812 (t-170)
  outliers start: 33
  outliers final: 25
  residues processed: 185
  average time/residue: 0.2654
  time to fit residues: 72.4836
Evaluate side-chains
  190 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 1.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  366 HIS
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  649 HIS
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  355 ASP
Chi-restraints excluded: chain B residue  366 HIS
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  649 HIS
Chi-restraints excluded: chain B residue  699 LYS
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain B residue  861 THR
Chi-restraints excluded: chain B residue  878 LEU
Chi-restraints excluded: chain B residue  887 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 145 optimal weight:    0.5980
   chunk 84 optimal weight:    0.0570
   chunk 83 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 24 optimal weight:    8.9990
   chunk 36 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 102 optimal weight:    2.9990
   chunk 137 optimal weight:    0.0470
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
B 712 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.122429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.099854 restraints weight = 22085.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.103863 restraints weight = 19106.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.104032 restraints weight = 15260.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.4523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  12374  Z= 0.105
  Angle     :  0.496   6.983  16708  Z= 0.260
  Chirality :  0.038   0.142   1948
  Planarity :  0.003   0.038   2096
  Dihedral  :  3.925  18.252   1662
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.29 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.22), residues: 1520
  helix:  2.17 (0.17), residues: 866
  sheet:  0.58 (0.40), residues: 156
  loop :  0.40 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 863 
 HIS   0.006   0.001   HIS A  85 
 PHE   0.019   0.001   PHE A 313 
 TYR   0.016   0.001   TYR B 667 
 ARG   0.008   0.000   ARG A 823 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03244 (  696)
  hydrogen bonds       : angle       4.04678 ( 2025)
  covalent geometry    : bond        0.00236 (12374)
  covalent geometry    : angle       0.49634 (16708)

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 170
  time to evaluate  : 1.302 
Fit side-chains
   revert: symmetry clash
REVERT: A  220 MET cc_start: 0.8163 (mtp) cc_final: 0.7869 (mtm)
REVERT: A  587 MET cc_start: 0.8145 (tpp) cc_final: 0.7829 (tpp)
REVERT: A  649 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.6734 (t-170)
REVERT: A  660 ASP cc_start: 0.7506 (t70) cc_final: 0.7242 (t70)
REVERT: A  874 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7633 (pt0)
REVERT: A  885 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7915 (tmm)
REVERT: B  172 MET cc_start: 0.7939 (mtt) cc_final: 0.7697 (mtt)
REVERT: B  587 MET cc_start: 0.8257 (tpp) cc_final: 0.7972 (tpp)
REVERT: B  649 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.5705 (t-170)
  outliers start: 33
  outliers final: 25
  residues processed: 188
  average time/residue: 0.2431
  time to fit residues: 65.4447
Evaluate side-chains
  192 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 164
  time to evaluate  : 1.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  366 HIS
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  649 HIS
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain A residue  885 MET
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  355 ASP
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  649 HIS
Chi-restraints excluded: chain B residue  699 LYS
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain B residue  861 THR
Chi-restraints excluded: chain B residue  878 LEU
Chi-restraints excluded: chain B residue  887 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 31 optimal weight:    0.2980
   chunk 141 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 122 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9980
   chunk 95 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 780 GLN
B 338 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.122030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.099680 restraints weight = 21967.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.103702 restraints weight = 18934.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.104026 restraints weight = 13926.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.4590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12374  Z= 0.113
  Angle     :  0.512   6.888  16708  Z= 0.267
  Chirality :  0.038   0.133   1948
  Planarity :  0.003   0.038   2096
  Dihedral  :  3.920  18.783   1662
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.44 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.22), residues: 1520
  helix:  2.15 (0.17), residues: 868
  sheet:  0.64 (0.40), residues: 156
  loop :  0.41 (0.30), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 863 
 HIS   0.006   0.001   HIS B 338 
 PHE   0.019   0.001   PHE A 313 
 TYR   0.018   0.001   TYR B 667 
 ARG   0.009   0.000   ARG B 823 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03287 (  696)
  hydrogen bonds       : angle       4.05063 ( 2025)
  covalent geometry    : bond        0.00259 (12374)
  covalent geometry    : angle       0.51210 (16708)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3996.22 seconds
wall clock time: 70 minutes 55.57 seconds (4255.57 seconds total)