Starting phenix.real_space_refine
on Sat Jan 18 09:58:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bh7_44535/01_2025/9bh7_44535.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bh7_44535/01_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_44535/01_2025/9bh7_44535.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bh7_44535/01_2025/9bh7_44535.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bh7_44535/01_2025/9bh7_44535.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bh7_44535/01_2025/9bh7_44535.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      80      5.16       5
     C    7776      2.51       5
     N    2112      2.21       5
     O    2198      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 12166
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6083
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 772, 6083
          Classifications: {'peptide': 772}
          Link IDs: {'PTRANS': 22, 'TRANS': 749}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 6083
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 772, 6083
          Classifications: {'peptide': 772}
          Link IDs: {'PTRANS': 22, 'TRANS': 749}
          Chain breaks: 5
  Time building chain proxies: 7.82, per 1000 atoms: 0.64
  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: 2.81
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 9 sheets defined
      63.1% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 74
    Processing helix  chain 'A' and resid 77 through 88
    Processing helix  chain 'A' and resid 93 through 102
    Processing helix  chain 'A' and resid 120 through 136
      removed outlier: 4.360A  pdb=" N   VAL A 124 " --> pdb=" O   GLY A 120 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   ALA A 125 " --> pdb=" O   LYS A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 165
      removed outlier: 3.976A  pdb=" N   GLU A 163 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   VAL A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 204
    Processing helix  chain 'A' and resid 205 through 208
      removed outlier: 4.591A  pdb=" N   ASP A 208 " --> pdb=" O   ASN A 205 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 205 through 208'
    Processing helix  chain 'A' and resid 217 through 223
      removed outlier: 3.896A  pdb=" N   GLY A 222 " --> pdb=" O   HIS A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 247
      removed outlier: 3.508A  pdb=" N   LEU A 229 " --> pdb=" O   HIS A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
    Processing helix  chain 'A' and resid 325 through 335
      removed outlier: 4.363A  pdb=" N   THR A 333 " --> pdb=" O   LEU A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 368
    Processing helix  chain 'A' and resid 383 through 396
    Processing helix  chain 'A' and resid 402 through 412
      removed outlier: 3.691A  pdb=" N   LYS A 407 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
      Proline residue:  A 410  - end of helix
    Processing helix  chain 'A' and resid 421 through 435
    Processing helix  chain 'A' and resid 444 through 449
      removed outlier: 3.806A  pdb=" N   SER A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 479
    Processing helix  chain 'A' and resid 500 through 510
    Processing helix  chain 'A' and resid 528 through 542
    Processing helix  chain 'A' and resid 546 through 557
    Processing helix  chain 'A' and resid 557 through 564
    Processing helix  chain 'A' and resid 578 through 592
    Processing helix  chain 'A' and resid 612 through 622
    Processing helix  chain 'A' and resid 624 through 640
      removed outlier: 3.990A  pdb=" N   ASP A 630 " --> pdb=" O   ALA A 626 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LYS A 640 " --> pdb=" O   GLN A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 655
    Processing helix  chain 'A' and resid 665 through 676
      removed outlier: 3.522A  pdb=" N   LYS A 675 " --> pdb=" O   CYS A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 688
    Processing helix  chain 'A' and resid 690 through 700
      removed outlier: 4.172A  pdb=" N   ARG A 696 " --> pdb=" O   GLY A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 729
    Processing helix  chain 'A' and resid 733 through 742
    Processing helix  chain 'A' and resid 744 through 770
    Processing helix  chain 'A' and resid 771 through 780
      removed outlier: 4.220A  pdb=" N   GLN A 780 " --> pdb=" O   LEU A 776 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 788
    Processing helix  chain 'A' and resid 790 through 794
      removed outlier: 3.508A  pdb=" N   CYS A 794 " --> pdb=" O   ARG A 791 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 795 through 799
    Processing helix  chain 'A' and resid 803 through 814
    Processing helix  chain 'A' and resid 817 through 824
    Processing helix  chain 'A' and resid 825 through 835
    Processing helix  chain 'A' and resid 871 through 892
    Processing helix  chain 'B' and resid 70 through 75
      removed outlier: 3.619A  pdb=" N   TRP B  74 " --> pdb=" O   LEU B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 87
      removed outlier: 3.683A  pdb=" N   LYS B  83 " --> pdb=" O   ALA B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 102
    Processing helix  chain 'B' and resid 120 through 136
      removed outlier: 4.155A  pdb=" N   VAL B 124 " --> pdb=" O   GLY B 120 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   ALA B 125 " --> pdb=" O   LYS B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 162
    Processing helix  chain 'B' and resid 163 through 165
      No H-bonds generated for 'chain 'B' and resid 163 through 165'
    Processing helix  chain 'B' and resid 180 through 184
    Processing helix  chain 'B' and resid 191 through 204
    Processing helix  chain 'B' and resid 206 through 208
      No H-bonds generated for 'chain 'B' and resid 206 through 208'
    Processing helix  chain 'B' and resid 219 through 224
      removed outlier: 4.308A  pdb=" N   ASP B 223 " --> pdb=" O   HIS B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 247
      removed outlier: 3.535A  pdb=" N   GLU B 231 " --> pdb=" O   GLY B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 278
    Processing helix  chain 'B' and resid 325 through 335
      removed outlier: 4.562A  pdb=" N   THR B 333 " --> pdb=" O   LEU B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 368
    Processing helix  chain 'B' and resid 383 through 396
      removed outlier: 3.923A  pdb=" N   LEU B 387 " --> pdb=" O   GLU B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 409
      removed outlier: 3.610A  pdb=" N   LYS B 407 " --> pdb=" O   SER B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 435
    Processing helix  chain 'B' and resid 443 through 450
      removed outlier: 4.324A  pdb=" N   SER B 447 " --> pdb=" O   THR B 443 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   SER B 448 " --> pdb=" O   SER B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 479
    Processing helix  chain 'B' and resid 500 through 510
    Processing helix  chain 'B' and resid 528 through 542
    Processing helix  chain 'B' and resid 546 through 557
    Processing helix  chain 'B' and resid 557 through 564
    Processing helix  chain 'B' and resid 578 through 592
    Processing helix  chain 'B' and resid 612 through 622
    Processing helix  chain 'B' and resid 624 through 640
      removed outlier: 4.010A  pdb=" N   ASP B 630 " --> pdb=" O   ALA B 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 647 through 655
    Processing helix  chain 'B' and resid 665 through 676
      removed outlier: 3.527A  pdb=" N   LYS B 675 " --> pdb=" O   CYS B 671 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 688
    Processing helix  chain 'B' and resid 690 through 700
    Processing helix  chain 'B' and resid 706 through 730
    Processing helix  chain 'B' and resid 733 through 742
    Processing helix  chain 'B' and resid 744 through 770
    Processing helix  chain 'B' and resid 771 through 788
      removed outlier: 3.613A  pdb=" N   LEU B 776 " --> pdb=" O   HIS B 772 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   GLN B 780 " --> pdb=" O   LEU B 776 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   PHE B 781 " --> pdb=" O   LEU B 777 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLN B 782 " --> pdb=" O   LEU B 778 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LYS B 783 " --> pdb=" O   SER B 779 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 790 through 796
      removed outlier: 4.161A  pdb=" N   ASP B 795 " --> pdb=" O   GLU B 792 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 814
    Processing helix  chain 'B' and resid 817 through 824
    Processing helix  chain 'B' and resid 825 through 836
    Processing helix  chain 'B' and resid 871 through 892
    Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171
      removed outlier: 6.645A  pdb=" N   ALA A 140 " --> pdb=" O   ALA A 187 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   CYS A 189 " --> pdb=" O   ALA A 140 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   PHE A 142 " --> pdb=" O   CYS A 189 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LYS A 139 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   VAL A 213 " --> pdb=" O   LYS A 139 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LEU A 141 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   VAL A 215 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ILE A 143 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 293
    Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 293
      removed outlier: 6.504A  pdb=" N   VAL A 457 " --> pdb=" O   ILE A 493 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   ILE A 495 " --> pdb=" O   VAL A 457 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ILE A 459 " --> pdb=" O   ILE A 495 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   LEU A 341 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   VAL A 340 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   ALA A 442 " --> pdb=" O   VAL A 340 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   LEU A 342 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   ALA A 414 " --> pdb=" O   ALA A 441 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 464
    Processing sheet with id=AA5, first strand: chain 'A' and resid 595 through 598
    Processing sheet with id=AA6, first strand: chain 'B' and resid 168 through 171
      removed outlier: 6.702A  pdb=" N   ALA B 140 " --> pdb=" O   ALA B 187 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   CYS B 189 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   PHE B 142 " --> pdb=" O   CYS B 189 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   LYS B 139 " --> pdb=" O   GLY B 211 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   VAL B 213 " --> pdb=" O   LYS B 139 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   LEU B 141 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 5.551A  pdb=" N   VAL B 215 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ILE B 143 " --> pdb=" O   VAL B 215 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   GLY B 211 " --> pdb=" O   GLN B 260 " (cutoff:3.500A)
      removed outlier: 8.205A  pdb=" N   VAL B 262 " --> pdb=" O   GLY B 211 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   VAL B 213 " --> pdb=" O   VAL B 262 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   MET B 264 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   VAL B 215 " --> pdb=" O   MET B 264 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 309 through 312
      removed outlier: 7.216A  pdb=" N   ILE B 302 " --> pdb=" O   VAL B 310 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   VAL B 457 " --> pdb=" O   ILE B 493 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   ILE B 495 " --> pdb=" O   VAL B 457 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ILE B 459 " --> pdb=" O   ILE B 495 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   VAL B 340 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   ALA B 442 " --> pdb=" O   VAL B 340 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   LEU B 342 " --> pdb=" O   ALA B 442 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ALA B 414 " --> pdb=" O   ALA B 441 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 463 through 464
    Processing sheet with id=AA9, first strand: chain 'B' and resid 595 through 598

    698 hydrogen bonds defined for protein.
    2025 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.36

  Time building geometry restraints manager: 3.31 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.410
  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:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     29.480
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.630
-------------------------------------------------------------------------------
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= 0.194
  Angle     :  0.635   6.393  16708  Z= 0.389
  Chirality :  0.045   0.165   1948
  Planarity :  0.007   0.086   2096
  Dihedral  : 12.657  88.633   4608
  Min Nonbonded Distance : 2.370

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

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

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

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

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 313
  time to evaluate  : 1.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6345 (mt-10)
REVERT: A  151 LYS cc_start: 0.8708 (mttt) cc_final: 0.8407 (mttp)
REVERT: A  557 THR cc_start: 0.8053 (m) cc_final: 0.7692 (p)
REVERT: B  126 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6505 (mt-10)
REVERT: B  151 LYS cc_start: 0.8800 (mttt) cc_final: 0.8511 (mttp)
REVERT: B  531 MET cc_start: 0.7282 (tpp) cc_final: 0.7028 (tpt)
REVERT: B  802 LEU cc_start: 0.8595 (tp) cc_final: 0.8372 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 313
  average time/residue: 0.3393
  time to fit residues: 139.4108
Evaluate side-chains
  172 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 130 optimal weight:    0.9990
   chunk 116 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 62 optimal weight:    0.6980
   chunk 120 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0060
   chunk 73 optimal weight:    0.0980
   chunk 89 optimal weight:    0.9980
   chunk 139 optimal weight:    1.9990
   overall best weight:    0.5196

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

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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.123743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.100475 restraints weight = 22120.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.102438 restraints weight = 16738.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.103148 restraints weight = 16445.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12374  Z= 0.192
  Angle     :  0.592  10.379  16708  Z= 0.318
  Chirality :  0.041   0.138   1948
  Planarity :  0.004   0.043   2096
  Dihedral  :  5.299  20.150   1662
  Min Nonbonded Distance : 2.599

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

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

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

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

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

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

  3040 Ramachandran restraints generated.
    1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 197
  time to evaluate  : 1.308 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8676 (tt)
REVERT: A  151 LYS cc_start: 0.8556 (mttt) cc_final: 0.8303 (mttp)
REVERT: A  154 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8158 (ttmm)
REVERT: A  167 LYS cc_start: 0.7912 (tppt) cc_final: 0.7543 (mmtm)
REVERT: A  331 TYR cc_start: 0.6849 (t80) cc_final: 0.6526 (t80)
REVERT: A  587 MET cc_start: 0.8254 (tpp) cc_final: 0.7871 (tpp)
REVERT: A  667 TYR cc_start: 0.8188 (t80) cc_final: 0.7981 (t80)
REVERT: B  151 LYS cc_start: 0.8675 (mttt) cc_final: 0.8455 (mttp)
REVERT: B  154 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8400 (ttmm)
  outliers start: 36
  outliers final: 16
  residues processed: 213
  average time/residue: 0.2682
  time to fit residues: 80.2530
Evaluate side-chains
  178 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 1.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  154 LYS
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  518 CYS
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  886 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   84 TYR
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  886 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 29 optimal weight:    0.0980
   chunk 113 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 112 optimal weight:    0.8980
   chunk 153 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 127 optimal weight:    2.9990
   chunk 32 optimal weight:    0.1980
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.121632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.098573 restraints weight = 22284.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.103503 restraints weight = 20900.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.103515 restraints weight = 14862.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.3360

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= 0.235
  Angle     :  0.558   9.361  16708  Z= 0.296
  Chirality :  0.040   0.133   1948
  Planarity :  0.004   0.041   2096
  Dihedral  :  4.837  17.055   1662
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 10.12 %
    Favored  : 87.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.21), residues: 1520
  helix:  1.20 (0.17), residues: 876
  sheet:  0.32 (0.38), residues: 166
  loop :  0.57 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 863 
 HIS   0.006   0.001   HIS A 416 
 PHE   0.021   0.002   PHE B 313 
 TYR   0.018   0.002   TYR A 228 
 ARG   0.004   0.000   ARG A 823 

*********************** 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
  214 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 184
  time to evaluate  : 1.455 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8729 (tt)
REVERT: A  151 LYS cc_start: 0.8498 (mttt) cc_final: 0.8232 (mttp)
REVERT: A  154 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8240 (ttpt)
REVERT: A  166 ILE cc_start: 0.8149 (mm) cc_final: 0.7711 (mt)
REVERT: A  167 LYS cc_start: 0.8055 (tppt) cc_final: 0.7740 (mmtm)
REVERT: B  130 LEU cc_start: 0.9099 (tp) cc_final: 0.8834 (tp)
REVERT: B  151 LYS cc_start: 0.8535 (mttt) cc_final: 0.8291 (mttm)
REVERT: B  172 MET cc_start: 0.7793 (mtt) cc_final: 0.7535 (mtt)
REVERT: B  316 MET cc_start: 0.7106 (ttp) cc_final: 0.6712 (mmt)
  outliers start: 30
  outliers final: 21
  residues processed: 200
  average time/residue: 0.2449
  time to fit residues: 70.4488
Evaluate side-chains
  185 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 162
  time to evaluate  : 1.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  154 LYS
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  189 CYS
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  355 ASP
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  861 THR
Chi-restraints excluded: chain B residue  886 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 106 optimal weight:    0.0060
   chunk 14 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 76 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 132 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.6596

-------------------------------------------------------------------------------
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 = 0.3922 r_free = 0.3922 target = 0.123045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.100235 restraints weight = 22146.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.104339 restraints weight = 19162.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.104507 restraints weight = 15292.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.3728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12374  Z= 0.181
  Angle     :  0.514   8.471  16708  Z= 0.273
  Chirality :  0.039   0.130   1948
  Planarity :  0.003   0.037   2096
  Dihedral  :  4.520  16.959   1662
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 11.62 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.21), residues: 1520
  helix:  1.52 (0.17), residues: 874
  sheet:  0.46 (0.37), residues: 176
  loop :  0.67 (0.30), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 863 
 HIS   0.004   0.001   HIS B 710 
 PHE   0.022   0.001   PHE A 313 
 TYR   0.020   0.002   TYR B 667 
 ARG   0.005   0.000   ARG B 745 

*********************** 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
  210 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 176
  time to evaluate  : 1.237 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 ILE cc_start: 0.8092 (mm) cc_final: 0.7664 (mt)
REVERT: A  167 LYS cc_start: 0.8149 (tppt) cc_final: 0.7855 (mmtm)
REVERT: A  649 HIS cc_start: 0.8318 (OUTLIER) cc_final: 0.6957 (t-170)
REVERT: B  130 LEU cc_start: 0.9123 (tp) cc_final: 0.8804 (tp)
REVERT: B  151 LYS cc_start: 0.8439 (mttt) cc_final: 0.8175 (mttp)
REVERT: B  172 MET cc_start: 0.7789 (mtt) cc_final: 0.7483 (mtt)
REVERT: B  587 MET cc_start: 0.8304 (tpp) cc_final: 0.7957 (tpp)
REVERT: B  649 HIS cc_start: 0.8423 (OUTLIER) cc_final: 0.6957 (t-170)
  outliers start: 34
  outliers final: 22
  residues processed: 193
  average time/residue: 0.2526
  time to fit residues: 70.2994
Evaluate side-chains
  182 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 158
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
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  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  164 VAL
Chi-restraints excluded: chain B residue  189 CYS
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain B residue  355 ASP
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  649 HIS
Chi-restraints excluded: chain B residue  878 LEU
Chi-restraints excluded: chain B residue  886 ILE
Chi-restraints excluded: chain B residue  887 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 76 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 115 optimal weight:    0.2980
   chunk 54 optimal weight:    0.0170
   chunk 26 optimal weight:    2.9990
   chunk 136 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.5218

-------------------------------------------------------------------------------
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 = 0.3926 r_free = 0.3926 target = 0.123288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.100506 restraints weight = 22089.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.104688 restraints weight = 18864.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.104794 restraints weight = 14948.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.4004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  12374  Z= 0.159
  Angle     :  0.501   7.397  16708  Z= 0.263
  Chirality :  0.038   0.127   1948
  Planarity :  0.003   0.038   2096
  Dihedral  :  4.252  16.997   1662
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 11.92 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.21), residues: 1520
  helix:  1.74 (0.17), residues: 874
  sheet:  0.66 (0.39), residues: 156
  loop :  0.59 (0.30), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 588 
 HIS   0.005   0.001   HIS B 710 
 PHE   0.021   0.001   PHE A 313 
 TYR   0.019   0.002   TYR B 667 
 ARG   0.006   0.000   ARG B 823 

*********************** 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
  218 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 180
  time to evaluate  : 1.446 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 LYS cc_start: 0.8168 (tppt) cc_final: 0.7874 (mmtm)
REVERT: A  220 MET cc_start: 0.8330 (mmm) cc_final: 0.7985 (mtp)
REVERT: A  316 MET cc_start: 0.6537 (ttt) cc_final: 0.6002 (mmt)
REVERT: A  549 ASP cc_start: 0.5555 (OUTLIER) cc_final: 0.5307 (t0)
REVERT: A  587 MET cc_start: 0.8211 (tpp) cc_final: 0.7872 (tpp)
REVERT: A  649 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.6750 (t-170)
REVERT: A  874 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7474 (pt0)
REVERT: B  151 LYS cc_start: 0.8462 (mttt) cc_final: 0.8161 (mttp)
REVERT: B  172 MET cc_start: 0.7835 (mtt) cc_final: 0.7514 (mtt)
REVERT: B  587 MET cc_start: 0.8293 (tpp) cc_final: 0.7968 (tpp)
REVERT: B  649 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.6873 (t-170)
  outliers start: 38
  outliers final: 21
  residues processed: 198
  average time/residue: 0.2658
  time to fit residues: 74.3756
Evaluate side-chains
  187 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 163
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  549 ASP
Chi-restraints excluded: chain A residue  649 HIS
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain A residue  886 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  189 CYS
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain B residue  355 ASP
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  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 112 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 106 optimal weight:    0.0020
   chunk 101 optimal weight:    7.9990
   chunk 149 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0050
   chunk 129 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.5804

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.122561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.099876 restraints weight = 22200.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.104627 restraints weight = 18620.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.104964 restraints weight = 11858.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  12374  Z= 0.164
  Angle     :  0.498   7.183  16708  Z= 0.259
  Chirality :  0.038   0.128   1948
  Planarity :  0.003   0.037   2096
  Dihedral  :  4.131  16.767   1662
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.34 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.22), residues: 1520
  helix:  1.92 (0.17), residues: 868
  sheet:  0.70 (0.39), residues: 156
  loop :  0.58 (0.30), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 863 
 HIS   0.005   0.001   HIS B 710 
 PHE   0.013   0.001   PHE A 313 
 TYR   0.016   0.002   TYR A 156 
 ARG   0.006   0.000   ARG B 823 

*********************** 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: 37
    poor density    : 172
  time to evaluate  : 1.329 
Fit side-chains
   revert: symmetry clash
REVERT: A  220 MET cc_start: 0.8268 (mmm) cc_final: 0.8047 (mtp)
REVERT: A  316 MET cc_start: 0.6570 (ttt) cc_final: 0.5889 (mmt)
REVERT: A  587 MET cc_start: 0.8196 (tpp) cc_final: 0.7855 (tpp)
REVERT: A  649 HIS cc_start: 0.8158 (OUTLIER) cc_final: 0.6653 (t-170)
REVERT: A  874 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7474 (pt0)
REVERT: A  885 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7888 (tmm)
REVERT: B  151 LYS cc_start: 0.8461 (mttt) cc_final: 0.8150 (mttp)
REVERT: B  172 MET cc_start: 0.7801 (mtt) cc_final: 0.7471 (mtt)
REVERT: B  347 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7912 (mtmt)
REVERT: B  426 ASP cc_start: 0.7911 (t0) cc_final: 0.7598 (t0)
REVERT: B  587 MET cc_start: 0.8290 (tpp) cc_final: 0.7966 (tpp)
REVERT: B  649 HIS cc_start: 0.8432 (OUTLIER) cc_final: 0.6855 (t-170)
REVERT: B  699 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7841 (tmtt)
  outliers start: 37
  outliers final: 21
  residues processed: 188
  average time/residue: 0.2470
  time to fit residues: 66.8475
Evaluate side-chains
  182 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 156
  time to evaluate  : 1.492 
-------------------------------------------------------------------------------
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  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  649 HIS
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain A residue  885 MET
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  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  886 ILE
Chi-restraints excluded: chain B residue  887 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 104 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 140 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 2 optimal weight:    6.9990
   chunk 63 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   chunk 19 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3910 r_free = 0.3910 target = 0.121978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.099321 restraints weight = 22169.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.102972 restraints weight = 19155.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.103374 restraints weight = 15659.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.4260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12374  Z= 0.177
  Angle     :  0.507   7.430  16708  Z= 0.263
  Chirality :  0.038   0.133   1948
  Planarity :  0.003   0.038   2096
  Dihedral  :  4.083  16.605   1662
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.32 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.22), residues: 1520
  helix:  1.98 (0.17), residues: 868
  sheet:  0.60 (0.39), residues: 156
  loop :  0.53 (0.30), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 863 
 HIS   0.004   0.001   HIS B 710 
 PHE   0.020   0.001   PHE A 815 
 TYR   0.015   0.002   TYR A 156 
 ARG   0.006   0.000   ARG A 823 

*********************** 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
  200 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 167
  time to evaluate  : 1.384 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8356 (ttmt)
REVERT: A  167 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7599 (mtmm)
REVERT: A  316 MET cc_start: 0.6408 (ttt) cc_final: 0.5945 (mmt)
REVERT: A  587 MET cc_start: 0.8207 (tpp) cc_final: 0.7873 (tpp)
REVERT: A  649 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.6675 (t-170)
REVERT: A  696 ARG cc_start: 0.8497 (ttp80) cc_final: 0.8289 (ttp80)
REVERT: A  885 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7915 (tmm)
REVERT: B  151 LYS cc_start: 0.8461 (mttt) cc_final: 0.8153 (mttp)
REVERT: B  172 MET cc_start: 0.7923 (mtt) cc_final: 0.7570 (mtt)
REVERT: B  347 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7948 (mtmt)
REVERT: B  426 ASP cc_start: 0.8032 (t0) cc_final: 0.7684 (t0)
REVERT: B  587 MET cc_start: 0.8305 (tpp) cc_final: 0.7985 (tpp)
REVERT: B  649 HIS cc_start: 0.8371 (OUTLIER) cc_final: 0.6785 (t-170)
  outliers start: 33
  outliers final: 25
  residues processed: 183
  average time/residue: 0.2532
  time to fit residues: 66.6607
Evaluate side-chains
  191 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 161
  time to evaluate  : 1.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  154 LYS
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  366 HIS
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  649 HIS
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain A residue  885 MET
Chi-restraints excluded: chain A residue  886 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain B residue  355 ASP
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  649 HIS
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain B residue  878 LEU
Chi-restraints excluded: chain B residue  886 ILE
Chi-restraints excluded: chain B residue  887 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 110 optimal weight:    0.0980
   chunk 53 optimal weight:    0.7980
   chunk 141 optimal weight:    0.8980
   chunk 132 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    0.3980
   chunk 136 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.5980

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.122727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.100075 restraints weight = 22321.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.103056 restraints weight = 19298.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.103423 restraints weight = 17970.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.4368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12374  Z= 0.168
  Angle     :  0.502   8.110  16708  Z= 0.261
  Chirality :  0.038   0.126   1948
  Planarity :  0.003   0.038   2096
  Dihedral  :  4.015  16.775   1662
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.54 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.22), residues: 1520
  helix:  2.05 (0.17), residues: 866
  sheet:  0.56 (0.39), residues: 156
  loop :  0.44 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 863 
 HIS   0.005   0.001   HIS A  85 
 PHE   0.017   0.001   PHE A 815 
 TYR   0.015   0.001   TYR A 171 
 ARG   0.007   0.000   ARG A 823 

*********************** 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
  199 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 166
  time to evaluate  : 1.492 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8331 (ttmt)
REVERT: A  307 MET cc_start: 0.6261 (tpp) cc_final: 0.6031 (tpp)
REVERT: A  587 MET cc_start: 0.8196 (tpp) cc_final: 0.7872 (tpp)
REVERT: A  649 HIS cc_start: 0.8152 (OUTLIER) cc_final: 0.6687 (t-170)
REVERT: A  660 ASP cc_start: 0.7570 (t70) cc_final: 0.7313 (t70)
REVERT: A  696 ARG cc_start: 0.8484 (ttp80) cc_final: 0.8270 (ttp80)
REVERT: A  885 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7934 (tmm)
REVERT: B  172 MET cc_start: 0.7878 (mtt) cc_final: 0.7600 (mtt)
REVERT: B  347 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7946 (mtmt)
REVERT: B  426 ASP cc_start: 0.8059 (t0) cc_final: 0.7712 (t0)
REVERT: B  587 MET cc_start: 0.8286 (tpp) cc_final: 0.7984 (tpp)
REVERT: B  649 HIS cc_start: 0.8380 (OUTLIER) cc_final: 0.5830 (t-170)
  outliers start: 33
  outliers final: 23
  residues processed: 183
  average time/residue: 0.2457
  time to fit residues: 65.1061
Evaluate side-chains
  189 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 1.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  154 LYS
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  366 HIS
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  649 HIS
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain A residue  885 MET
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain B residue  355 ASP
Chi-restraints excluded: chain B residue  366 HIS
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 100 optimal weight:    0.7980
   chunk 96 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 109 optimal weight:    0.8980
   chunk 146 optimal weight:    0.9980
   chunk 140 optimal weight:    0.4980
   chunk 22 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 130 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 25 optimal weight:    0.1980
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.122273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.099917 restraints weight = 22141.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.102804 restraints weight = 20002.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.103241 restraints weight = 18033.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.4440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12374  Z= 0.172
  Angle     :  0.507   6.976  16708  Z= 0.263
  Chirality :  0.038   0.166   1948
  Planarity :  0.003   0.038   2096
  Dihedral  :  3.971  18.429   1662
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.54 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.22), residues: 1520
  helix:  2.07 (0.17), residues: 868
  sheet:  0.52 (0.39), residues: 156
  loop :  0.41 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 863 
 HIS   0.006   0.001   HIS A  85 
 PHE   0.022   0.001   PHE A 313 
 TYR   0.017   0.002   TYR B 667 
 ARG   0.008   0.000   ARG A 823 

*********************** 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
  203 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 167
  time to evaluate  : 1.436 
Fit side-chains
   revert: symmetry clash
REVERT: A  220 MET cc_start: 0.8105 (mtp) cc_final: 0.7823 (mtm)
REVERT: A  307 MET cc_start: 0.6259 (tpp) cc_final: 0.6041 (tpp)
REVERT: A  587 MET cc_start: 0.8162 (tpp) cc_final: 0.7850 (tpp)
REVERT: A  649 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.6766 (t-170)
REVERT: A  660 ASP cc_start: 0.7464 (t70) cc_final: 0.7211 (t70)
REVERT: A  885 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7876 (tmm)
REVERT: B  172 MET cc_start: 0.7924 (mtt) cc_final: 0.7636 (mtt)
REVERT: B  426 ASP cc_start: 0.8043 (t0) cc_final: 0.7700 (t0)
REVERT: B  587 MET cc_start: 0.8255 (tpp) cc_final: 0.7967 (tpp)
REVERT: B  649 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.5862 (t-170)
REVERT: B  874 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7449 (pt0)
  outliers start: 36
  outliers final: 27
  residues processed: 185
  average time/residue: 0.2501
  time to fit residues: 66.6734
Evaluate side-chains
  189 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 159
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
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  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  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  878 LEU
Chi-restraints excluded: chain B residue  886 ILE
Chi-restraints excluded: chain B residue  887 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 145 optimal weight:    0.6980
   chunk 84 optimal weight:    0.6980
   chunk 83 optimal weight:    0.6980
   chunk 89 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0770
   chunk 36 optimal weight:    9.9990
   chunk 26 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 102 optimal weight:    2.9990
   chunk 137 optimal weight:    0.0980
   overall best weight:    0.4538

-------------------------------------------------------------------------------
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 = 0.3921 r_free = 0.3921 target = 0.122745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.100356 restraints weight = 22132.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.103591 restraints weight = 19918.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.104126 restraints weight = 15630.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.4530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  12374  Z= 0.156
  Angle     :  0.517   8.942  16708  Z= 0.271
  Chirality :  0.038   0.236   1948
  Planarity :  0.003   0.037   2096
  Dihedral  :  3.913  18.617   1662
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 15.22 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.22), residues: 1520
  helix:  2.15 (0.17), residues: 868
  sheet:  0.60 (0.39), residues: 156
  loop :  0.39 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 863 
 HIS   0.007   0.001   HIS A  85 
 PHE   0.020   0.001   PHE A 313 
 TYR   0.017   0.001   TYR B 667 
 ARG   0.009   0.000   ARG B 823 

********************** 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
  196 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 168
  time to evaluate  : 1.384 
Fit side-chains
   revert: symmetry clash
REVERT: A  220 MET cc_start: 0.8149 (mtp) cc_final: 0.7856 (mtm)
REVERT: A  587 MET cc_start: 0.8129 (tpp) cc_final: 0.7822 (tpp)
REVERT: A  649 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.6683 (t-170)
REVERT: A  657 MET cc_start: 0.7456 (mmt) cc_final: 0.7222 (tpt)
REVERT: A  660 ASP cc_start: 0.7517 (t70) cc_final: 0.7259 (t70)
REVERT: A  696 ARG cc_start: 0.8500 (ttp80) cc_final: 0.8294 (ttp80)
REVERT: A  885 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7868 (tmm)
REVERT: B  172 MET cc_start: 0.7883 (mtt) cc_final: 0.7601 (mtt)
REVERT: B  426 ASP cc_start: 0.8021 (t0) cc_final: 0.7670 (t0)
REVERT: B  587 MET cc_start: 0.8211 (tpp) cc_final: 0.7938 (tpp)
REVERT: B  649 HIS cc_start: 0.8453 (OUTLIER) cc_final: 0.5870 (t-170)
REVERT: B  874 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7467 (pt0)
  outliers start: 28
  outliers final: 24
  residues processed: 182
  average time/residue: 0.2454
  time to fit residues: 64.8663
Evaluate side-chains
  190 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 1.408 
-------------------------------------------------------------------------------
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  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  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  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 31 optimal weight:    0.6980
   chunk 141 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 105 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 610 HIS
A 780 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.121362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.099184 restraints weight = 22125.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.101681 restraints weight = 20546.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.102344 restraints weight = 16627.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.4541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12374  Z= 0.200
  Angle     :  0.527   8.202  16708  Z= 0.274
  Chirality :  0.039   0.208   1948
  Planarity :  0.003   0.039   2096
  Dihedral  :  3.978  17.515   1662
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.99 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.22), residues: 1520
  helix:  2.08 (0.17), residues: 872
  sheet:  0.55 (0.40), residues: 156
  loop :  0.28 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 863 
 HIS   0.007   0.001   HIS A  85 
 PHE   0.018   0.001   PHE A 313 
 TYR   0.016   0.002   TYR B 667 
 ARG   0.008   0.000   ARG A 823 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3461.73 seconds
wall clock time: 62 minutes 57.12 seconds (3777.12 seconds total)