Starting phenix.real_space_refine
on Sat Aug 23 12:38:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bh7_44535/08_2025/9bh7_44535.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bh7_44535/08_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_44535/08_2025/9bh7_44535.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bh7_44535/08_2025/9bh7_44535.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bh7_44535/08_2025/9bh7_44535.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bh7_44535/08_2025/9bh7_44535.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.32, per 1000 atoms: 0.27
  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: 0.88
  Conformation dependent library (CDL) restraints added in 498.1 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.40
  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: 1.98

  Time building geometry restraints manager: 1.21 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: 0.02
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:             2.170
  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:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.190
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.260
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.019   0.003   ARG B 745 
 TYR   0.026   0.004   TYR A 758 
 PHE   0.015   0.002   PHE B 632 
 TRP   0.021   0.002   TRP B 863 
 HIS   0.006   0.001   HIS B 710 

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

*********************** 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  : 0.561 
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: 0.6346 (mt-10)
REVERT: A  151 LYS cc_start: 0.8708 (mttt) cc_final: 0.8409 (mttp)
REVERT: A  557 THR cc_start: 0.8053 (m) cc_final: 0.7694 (p)
REVERT: B  126 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6501 (mt-10)
REVERT: B  151 LYS cc_start: 0.8800 (mttt) cc_final: 0.8475 (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: 0.1519
  time to fit residues: 62.9540
Evaluate side-chains
  171 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3910 r_free = 0.3910 target = 0.121992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.099360 restraints weight = 22223.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.103078 restraints weight = 18131.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.103262 restraints weight = 15418.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.105044 restraints weight = 10292.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.105141 restraints weight = 8420.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12374  Z= 0.157
  Angle     :  0.608  10.990  16708  Z= 0.325
  Chirality :  0.042   0.137   1948
  Planarity :  0.004   0.043   2096
  Dihedral  :  5.388  20.217   1662
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  :  6.67 %
    Favored  : 90.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.21), residues: 1520
  helix:  0.72 (0.16), residues: 888
  sheet:  0.69 (0.40), residues: 154
  loop :  0.32 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 438 
 TYR   0.025   0.002   TYR A 228 
 PHE   0.022   0.002   PHE A 313 
 TRP   0.010   0.001   TRP A  95 
 HIS   0.009   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (12374)
  covalent geometry    : angle       0.60760 (16708)
  hydrogen bonds       : bond        0.04759 (  696)
  hydrogen bonds       : angle       4.93001 ( 2025)

*********************** 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
  228 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 192
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8662 (tt)
REVERT: A  151 LYS cc_start: 0.8593 (mttt) cc_final: 0.8228 (mttp)
REVERT: A  167 LYS cc_start: 0.7869 (tppt) cc_final: 0.7459 (mmtm)
REVERT: A  667 TYR cc_start: 0.8100 (t80) cc_final: 0.7900 (t80)
REVERT: B  151 LYS cc_start: 0.8695 (mttt) cc_final: 0.8413 (mttp)
REVERT: B  313 PHE cc_start: 0.7545 (t80) cc_final: 0.7341 (t80)
REVERT: B  872 GLU cc_start: 0.8051 (mp0) cc_final: 0.7671 (mp0)
  outliers start: 36
  outliers final: 19
  residues processed: 208
  average time/residue: 0.1118
  time to fit residues: 32.4646
Evaluate side-chains
  179 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 159
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
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  191 ILE
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  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  355 ASP
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 132 optimal weight:    0.8980
   chunk 126 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 129 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 92 optimal weight:    3.9990
   chunk 117 optimal weight:    0.9980
   chunk 141 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A  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 = 0.3890 r_free = 0.3890 target = 0.120816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.098538 restraints weight = 22450.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.101629 restraints weight = 21796.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.102309 restraints weight = 16741.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.103633 restraints weight = 10517.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.104364 restraints weight = 9218.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12374  Z= 0.161
  Angle     :  0.569   9.687  16708  Z= 0.301
  Chirality :  0.041   0.132   1948
  Planarity :  0.004   0.041   2096
  Dihedral  :  4.954  17.601   1662
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  :  9.97 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.21), residues: 1520
  helix:  1.16 (0.17), residues: 874
  sheet:  0.42 (0.38), residues: 166
  loop :  0.57 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 823 
 TYR   0.021   0.002   TYR A 228 
 PHE   0.023   0.002   PHE A 313 
 TRP   0.007   0.001   TRP B 863 
 HIS   0.006   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (12374)
  covalent geometry    : angle       0.56852 (16708)
  hydrogen bonds       : bond        0.04329 (  696)
  hydrogen bonds       : angle       4.72306 ( 2025)

*********************** 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
  207 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 176
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8682 (tt)
REVERT: A  151 LYS cc_start: 0.8657 (mttt) cc_final: 0.8387 (mttm)
REVERT: A  166 ILE cc_start: 0.8208 (mm) cc_final: 0.7773 (mt)
REVERT: A  167 LYS cc_start: 0.8018 (tppt) cc_final: 0.7719 (mmtm)
REVERT: A  225 HIS cc_start: 0.5830 (m90) cc_final: 0.5261 (m-70)
REVERT: B  130 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8716 (tp)
REVERT: B  151 LYS cc_start: 0.8641 (mttt) cc_final: 0.8381 (mttp)
REVERT: B  587 MET cc_start: 0.8357 (tpp) cc_final: 0.7998 (tpp)
  outliers start: 31
  outliers final: 20
  residues processed: 191
  average time/residue: 0.1128
  time to fit residues: 31.2777
Evaluate side-chains
  179 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
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  176 SER
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 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  204 GLU
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  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 137 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   chunk 131 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0270
   chunk 148 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.7640

-------------------------------------------------------------------------------
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 = 0.3908 r_free = 0.3908 target = 0.121989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.099292 restraints weight = 22264.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.103678 restraints weight = 19259.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.103999 restraints weight = 14485.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.104664 restraints weight = 9843.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.106699 restraints weight = 8836.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12374  Z= 0.130
  Angle     :  0.518   8.705  16708  Z= 0.276
  Chirality :  0.039   0.131   1948
  Planarity :  0.003   0.038   2096
  Dihedral  :  4.592  17.814   1662
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 11.32 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.21), residues: 1520
  helix:  1.44 (0.17), residues: 874
  sheet:  0.70 (0.39), residues: 156
  loop :  0.54 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 823 
 TYR   0.020   0.002   TYR A 228 
 PHE   0.016   0.002   PHE A 765 
 TRP   0.007   0.001   TRP A 863 
 HIS   0.004   0.001   HIS B 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (12374)
  covalent geometry    : angle       0.51799 (16708)
  hydrogen bonds       : bond        0.03834 (  696)
  hydrogen bonds       : angle       4.48295 ( 2025)

*********************** 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
  213 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 174
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 ILE cc_start: 0.8125 (mm) cc_final: 0.7714 (mt)
REVERT: A  167 LYS cc_start: 0.8100 (tppt) cc_final: 0.7815 (mmtm)
REVERT: A  225 HIS cc_start: 0.5775 (m90) cc_final: 0.5491 (m-70)
REVERT: A  649 HIS cc_start: 0.8322 (OUTLIER) cc_final: 0.6912 (t-170)
REVERT: B  130 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8671 (tp)
REVERT: B  172 MET cc_start: 0.7776 (mtt) cc_final: 0.7480 (mtt)
REVERT: B  587 MET cc_start: 0.8367 (tpp) cc_final: 0.8044 (tpp)
REVERT: B  649 HIS cc_start: 0.8333 (OUTLIER) cc_final: 0.6822 (t-170)
  outliers start: 39
  outliers final: 24
  residues processed: 193
  average time/residue: 0.1101
  time to fit residues: 30.8461
Evaluate side-chains
  182 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
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  176 SER
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  286 ASP
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  582 ILE
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  130 LEU
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  189 CYS
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  829 VAL
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 56 optimal weight:    3.9990
   chunk 153 optimal weight:   10.0000
   chunk 37 optimal weight:    0.5980
   chunk 149 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0060
   chunk 88 optimal weight:    1.9990
   chunk 91 optimal weight:    0.4980
   chunk 113 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.5598

-------------------------------------------------------------------------------
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 = 0.122724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.099843 restraints weight = 22296.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.103352 restraints weight = 19272.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.103643 restraints weight = 17016.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.105107 restraints weight = 10557.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.105438 restraints weight = 9089.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.3982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12374  Z= 0.114
  Angle     :  0.499   7.705  16708  Z= 0.265
  Chirality :  0.038   0.129   1948
  Planarity :  0.003   0.037   2096
  Dihedral  :  4.332  16.153   1662
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 12.82 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.21), residues: 1520
  helix:  1.68 (0.17), residues: 872
  sheet:  0.77 (0.39), residues: 156
  loop :  0.50 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 823 
 TYR   0.022   0.002   TYR B 667 
 PHE   0.021   0.001   PHE B 313 
 TRP   0.006   0.001   TRP A  95 
 HIS   0.005   0.001   HIS B 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (12374)
  covalent geometry    : angle       0.49930 (16708)
  hydrogen bonds       : bond        0.03597 (  696)
  hydrogen bonds       : angle       4.32716 ( 2025)

*********************** 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
  209 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 175
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 LYS cc_start: 0.8155 (tppt) cc_final: 0.7868 (mmtm)
REVERT: A  225 HIS cc_start: 0.6020 (m90) cc_final: 0.5782 (m-70)
REVERT: A  587 MET cc_start: 0.8195 (tpp) cc_final: 0.7882 (tpp)
REVERT: A  649 HIS cc_start: 0.8231 (OUTLIER) cc_final: 0.6799 (t-170)
REVERT: A  874 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7382 (pt0)
REVERT: B  172 MET cc_start: 0.7819 (mtt) cc_final: 0.7401 (mtt)
REVERT: B  316 MET cc_start: 0.7047 (ttt) cc_final: 0.6548 (mmt)
REVERT: B  587 MET cc_start: 0.8344 (tpp) cc_final: 0.8057 (tpp)
REVERT: B  649 HIS cc_start: 0.8419 (OUTLIER) cc_final: 0.6888 (t-170)
  outliers start: 34
  outliers final: 19
  residues processed: 192
  average time/residue: 0.1199
  time to fit residues: 33.1683
Evaluate side-chains
  177 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
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  512 LEU
Chi-restraints excluded: chain A residue  527 VAL
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  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  829 VAL
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 20 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 107 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 144 optimal weight:    0.9990
   chunk 132 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3904 r_free = 0.3904 target = 0.121568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.098965 restraints weight = 22124.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.103544 restraints weight = 18987.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.103734 restraints weight = 14042.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.104377 restraints weight = 9540.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.105536 restraints weight = 8562.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.4117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12374  Z= 0.128
  Angle     :  0.512   8.024  16708  Z= 0.267
  Chirality :  0.039   0.129   1948
  Planarity :  0.003   0.038   2096
  Dihedral  :  4.260  16.436   1662
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 13.57 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.22), residues: 1520
  helix:  1.83 (0.17), residues: 866
  sheet:  0.84 (0.40), residues: 156
  loop :  0.47 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 823 
 TYR   0.019   0.002   TYR A 228 
 PHE   0.022   0.001   PHE A 815 
 TRP   0.007   0.001   TRP A 863 
 HIS   0.004   0.001   HIS B 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (12374)
  covalent geometry    : angle       0.51210 (16708)
  hydrogen bonds       : bond        0.03634 (  696)
  hydrogen bonds       : angle       4.25627 ( 2025)

*********************** 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
  209 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 170
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: A  180 HIS cc_start: 0.7694 (m170) cc_final: 0.7385 (m170)
REVERT: A  220 MET cc_start: 0.8274 (mmm) cc_final: 0.7930 (mtp)
REVERT: A  225 HIS cc_start: 0.5960 (m90) cc_final: 0.5707 (m-70)
REVERT: A  531 MET cc_start: 0.6691 (tpt) cc_final: 0.6416 (tpt)
REVERT: A  649 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.6747 (t-170)
REVERT: A  885 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7853 (tmm)
REVERT: B  172 MET cc_start: 0.7939 (mtt) cc_final: 0.7616 (mtt)
REVERT: B  587 MET cc_start: 0.8351 (tpp) cc_final: 0.8048 (tpp)
REVERT: B  649 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.6842 (t-170)
REVERT: B  699 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7882 (tmtt)
  outliers start: 39
  outliers final: 25
  residues processed: 191
  average time/residue: 0.1214
  time to fit residues: 33.1238
Evaluate side-chains
  192 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 163
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
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  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  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  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  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  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 45 optimal weight:    0.5980
   chunk 96 optimal weight:    0.8980
   chunk 106 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 131 optimal weight:    0.0970
   chunk 87 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    8.9990
   chunk 71 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.6378

-------------------------------------------------------------------------------
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 = 0.3907 r_free = 0.3907 target = 0.121987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.099767 restraints weight = 22129.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.103800 restraints weight = 19436.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.104133 restraints weight = 14532.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.106157 restraints weight = 9951.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.106219 restraints weight = 7923.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.4266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12374  Z= 0.115
  Angle     :  0.494   7.644  16708  Z= 0.259
  Chirality :  0.038   0.127   1948
  Planarity :  0.003   0.039   2096
  Dihedral  :  4.116  16.537   1662
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.47 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.22), residues: 1520
  helix:  1.95 (0.17), residues: 866
  sheet:  0.87 (0.40), residues: 156
  loop :  0.43 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 823 
 TYR   0.018   0.001   TYR B 667 
 PHE   0.016   0.001   PHE A 815 
 TRP   0.007   0.001   TRP A 863 
 HIS   0.005   0.001   HIS B 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (12374)
  covalent geometry    : angle       0.49419 (16708)
  hydrogen bonds       : bond        0.03458 (  696)
  hydrogen bonds       : angle       4.17381 ( 2025)

*********************** 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
  197 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 169
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A  167 LYS cc_start: 0.8200 (mmtm) cc_final: 0.7589 (mtmm)
REVERT: A  225 HIS cc_start: 0.5932 (m90) cc_final: 0.5598 (m-70)
REVERT: A  649 HIS cc_start: 0.8231 (OUTLIER) cc_final: 0.6727 (t-170)
REVERT: A  885 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7843 (tmm)
REVERT: B  172 MET cc_start: 0.7880 (mtt) cc_final: 0.7505 (mtt)
REVERT: B  316 MET cc_start: 0.6781 (ttt) cc_final: 0.6378 (mmt)
REVERT: B  347 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7906 (mtmt)
REVERT: B  587 MET cc_start: 0.8307 (tpp) cc_final: 0.8032 (tpp)
REVERT: B  649 HIS cc_start: 0.8462 (OUTLIER) cc_final: 0.5870 (t-170)
  outliers start: 28
  outliers final: 20
  residues processed: 183
  average time/residue: 0.1268
  time to fit residues: 32.8009
Evaluate side-chains
  186 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
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  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  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  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  649 HIS
Chi-restraints excluded: chain B residue  829 VAL
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 77 optimal weight:   10.0000
   chunk 79 optimal weight:    0.6980
   chunk 111 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 133 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 610 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.121465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.098941 restraints weight = 22158.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.101837 restraints weight = 20345.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.102583 restraints weight = 17059.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.103714 restraints weight = 10599.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.104260 restraints weight = 9433.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.4363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12374  Z= 0.128
  Angle     :  0.514   8.402  16708  Z= 0.266
  Chirality :  0.039   0.140   1948
  Planarity :  0.003   0.039   2096
  Dihedral  :  4.101  16.696   1662
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.22), residues: 1520
  helix:  1.94 (0.17), residues: 868
  sheet:  0.79 (0.40), residues: 156
  loop :  0.38 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 823 
 TYR   0.016   0.002   TYR B 667 
 PHE   0.014   0.001   PHE A 815 
 TRP   0.006   0.001   TRP A 863 
 HIS   0.008   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (12374)
  covalent geometry    : angle       0.51440 (16708)
  hydrogen bonds       : bond        0.03519 (  696)
  hydrogen bonds       : angle       4.16702 ( 2025)

*********************** 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
  204 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 170
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A  217 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8070 (mm-30)
REVERT: A  225 HIS cc_start: 0.6182 (m90) cc_final: 0.5918 (m-70)
REVERT: A  307 MET cc_start: 0.6123 (tpp) cc_final: 0.5898 (tpp)
REVERT: A  649 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.6774 (t-170)
REVERT: A  660 ASP cc_start: 0.7426 (t70) cc_final: 0.7180 (t70)
REVERT: A  885 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7869 (tmm)
REVERT: B  172 MET cc_start: 0.7892 (mtt) cc_final: 0.7494 (mtt)
REVERT: B  587 MET cc_start: 0.8313 (tpp) cc_final: 0.8075 (tpp)
REVERT: B  649 HIS cc_start: 0.8402 (OUTLIER) cc_final: 0.5720 (t-170)
  outliers start: 34
  outliers final: 26
  residues processed: 187
  average time/residue: 0.1192
  time to fit residues: 31.9675
Evaluate side-chains
  191 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 162
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
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  286 ASP
Chi-restraints excluded: chain A residue  302 ILE
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  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  654 VAL
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  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  829 VAL
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 125 optimal weight:    0.0570
   chunk 14 optimal weight:    0.4980
   chunk 50 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 123 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 149 optimal weight:    2.9990
   chunk 139 optimal weight:    0.5980
   chunk 94 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
A 551 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.122382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.099657 restraints weight = 22121.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.104614 restraints weight = 17501.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.104788 restraints weight = 11999.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.105689 restraints weight = 8805.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.106068 restraints weight = 7767.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.4504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12374  Z= 0.109
  Angle     :  0.498   8.923  16708  Z= 0.259
  Chirality :  0.038   0.131   1948
  Planarity :  0.003   0.039   2096
  Dihedral  :  4.002  16.638   1662
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.82 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.00 (0.22), residues: 1520
  helix:  2.03 (0.17), residues: 866
  sheet:  0.80 (0.41), residues: 156
  loop :  0.35 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 823 
 TYR   0.021   0.001   TYR A 228 
 PHE   0.022   0.001   PHE A 313 
 TRP   0.007   0.001   TRP A 863 
 HIS   0.006   0.001   HIS A  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (12374)
  covalent geometry    : angle       0.49842 (16708)
  hydrogen bonds       : bond        0.03382 (  696)
  hydrogen bonds       : angle       4.13046 ( 2025)

*********************** 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
  200 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 170
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A  225 HIS cc_start: 0.6118 (m90) cc_final: 0.5860 (m-70)
REVERT: A  231 GLU cc_start: 0.7796 (tp30) cc_final: 0.7367 (tp30)
REVERT: A  587 MET cc_start: 0.8170 (tpp) cc_final: 0.7873 (tpp)
REVERT: A  649 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.6614 (t-170)
REVERT: A  660 ASP cc_start: 0.7363 (t70) cc_final: 0.7126 (t70)
REVERT: A  885 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7845 (tmm)
REVERT: B  172 MET cc_start: 0.7868 (mtt) cc_final: 0.7465 (mtt)
REVERT: B  347 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7937 (mtmt)
REVERT: B  587 MET cc_start: 0.8291 (tpp) cc_final: 0.8049 (tpp)
REVERT: B  649 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.5750 (t-170)
REVERT: B  874 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7470 (pt0)
  outliers start: 30
  outliers final: 23
  residues processed: 187
  average time/residue: 0.1177
  time to fit residues: 31.7507
Evaluate side-chains
  187 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 160
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
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  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  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  654 VAL
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  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  649 HIS
Chi-restraints excluded: chain B residue  829 VAL
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 54 optimal weight:    0.9990
   chunk 137 optimal weight:    0.0060
   chunk 40 optimal weight:    0.1980
   chunk 77 optimal weight:   10.0000
   chunk 17 optimal weight:    0.7980
   chunk 33 optimal weight:    0.3980
   chunk 112 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 119 optimal weight:    0.9980
   chunk 144 optimal weight:    0.5980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.3996

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.122768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.100406 restraints weight = 22233.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.102135 restraints weight = 19161.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.103545 restraints weight = 13786.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.105534 restraints weight = 10636.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.105897 restraints weight = 9568.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.4630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  12374  Z= 0.105
  Angle     :  0.513   8.662  16708  Z= 0.264
  Chirality :  0.038   0.132   1948
  Planarity :  0.003   0.038   2096
  Dihedral  :  3.927  16.624   1662
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 16.04 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.22), residues: 1520
  helix:  2.10 (0.17), residues: 866
  sheet:  1.02 (0.41), residues: 152
  loop :  0.26 (0.29), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 823 
 TYR   0.017   0.001   TYR B 667 
 PHE   0.022   0.001   PHE A 313 
 TRP   0.006   0.001   TRP A 863 
 HIS   0.007   0.001   HIS A  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (12374)
  covalent geometry    : angle       0.51299 (16708)
  hydrogen bonds       : bond        0.03310 (  696)
  hydrogen bonds       : angle       4.08587 ( 2025)

********************** 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
  201 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 173
  time to evaluate  : 0.555 
Fit side-chains
REVERT: A  225 HIS cc_start: 0.6140 (m90) cc_final: 0.5865 (m-70)
REVERT: A  587 MET cc_start: 0.8159 (tpp) cc_final: 0.7871 (tpp)
REVERT: A  649 HIS cc_start: 0.8202 (OUTLIER) cc_final: 0.6685 (t-170)
REVERT: A  885 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7827 (tmm)
REVERT: B  172 MET cc_start: 0.7850 (mtt) cc_final: 0.7440 (mtt)
REVERT: B  587 MET cc_start: 0.8279 (tpp) cc_final: 0.8064 (tpp)
REVERT: B  649 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.5855 (t-170)
REVERT: B  874 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7597 (pt0)
  outliers start: 28
  outliers final: 21
  residues processed: 186
  average time/residue: 0.1182
  time to fit residues: 31.6618
Evaluate side-chains
  183 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 159
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
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  286 ASP
Chi-restraints excluded: chain A residue  302 ILE
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  654 VAL
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  134 LEU
Chi-restraints excluded: chain B residue  191 ILE
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  829 VAL
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 1 optimal weight:    0.9980
   chunk 75 optimal weight:    6.9990
   chunk 135 optimal weight:    0.4980
   chunk 57 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9980
   chunk 107 optimal weight:    0.8980
   chunk 108 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 77 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.121280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.098981 restraints weight = 22171.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.102505 restraints weight = 19811.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.102688 restraints weight = 17183.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.103772 restraints weight = 10766.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.105019 restraints weight = 9318.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.4651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12374  Z= 0.124
  Angle     :  0.522   7.368  16708  Z= 0.270
  Chirality :  0.038   0.125   1948
  Planarity :  0.004   0.040   2096
  Dihedral  :  3.974  16.753   1662
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 16.04 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.22), residues: 1520
  helix:  2.07 (0.17), residues: 868
  sheet:  0.79 (0.41), residues: 156
  loop :  0.31 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 823 
 TYR   0.021   0.002   TYR A 228 
 PHE   0.024   0.001   PHE A 313 
 TRP   0.006   0.001   TRP A 863 
 HIS   0.008   0.001   HIS A 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (12374)
  covalent geometry    : angle       0.52207 (16708)
  hydrogen bonds       : bond        0.03431 (  696)
  hydrogen bonds       : angle       4.12093 ( 2025)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1945.58 seconds
wall clock time: 34 minutes 32.74 seconds (2072.74 seconds total)