Starting phenix.real_space_refine
on Mon Dec 30 00:49:05 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b8j_15914/12_2024/8b8j_15914.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b8j_15914/12_2024/8b8j_15914.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b8j_15914/12_2024/8b8j_15914.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b8j_15914/12_2024/8b8j_15914.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b8j_15914/12_2024/8b8j_15914.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b8j_15914/12_2024/8b8j_15914.cif"
  }
  resolution = 2.96
  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=   0.001 sd=   0.019
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: 5
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     S      76      5.16       5
     C    7686      2.51       5
     N    1884      2.21       5
     O    2034      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 11686
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 709, 5840
          Classifications: {'peptide': 709}
          Link IDs: {'PTRANS': 32, 'TRANS': 676}
          Chain breaks: 8
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B
  Time building chain proxies: 12.00, per 1000 atoms: 1.03
  Number of scatterers: 11686
  At special positions: 0
  Unit cell: (126.294, 83.328, 113.274, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      6     19.99
     S      76     16.00
     O    2034      8.00
     N    1884      7.00
     C    7686      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 331 " - pdb=" SG  CYS A 372 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 338 " - pdb=" SG  CYS A 365 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 349 " - pdb=" SG  CYS A 807 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 352 " - pdb=" SG  CYS A 356 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.03
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2696

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 8 sheets defined
      64.7% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 108
    Processing helix  chain 'A' and resid 131 through 142
    Processing helix  chain 'A' and resid 205 through 220
    Processing helix  chain 'A' and resid 234 through 239
    Processing helix  chain 'A' and resid 264 through 273
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 284 through 293
    Processing helix  chain 'A' and resid 293 through 327
    Processing helix  chain 'A' and resid 331 through 339
    Processing helix  chain 'A' and resid 364 through 375
      removed outlier: 3.513A  pdb=" N   ILE A 373 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 409
    Processing helix  chain 'A' and resid 447 through 473
    Processing helix  chain 'A' and resid 474 through 488
    Processing helix  chain 'A' and resid 504 through 539
      removed outlier: 3.568A  pdb=" N   ALA A 508 " --> pdb=" O   THR A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 573
      removed outlier: 5.505A  pdb=" N   SER A 566 " --> pdb=" O   ASN A 562 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   CYS A 567 " --> pdb=" O   TYR A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 638
      removed outlier: 3.880A  pdb=" N   LYS A 616 " --> pdb=" O   ILE A 612 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ALA A 617 " --> pdb=" O   MET A 613 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ILE A 618 " --> pdb=" O   GLY A 614 " (cutoff:3.500A)
      Proline residue:  A 628  - end of helix
      removed outlier: 3.525A  pdb=" N   GLY A 635 " --> pdb=" O   MET A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 655
    Processing helix  chain 'A' and resid 662 through 681
      removed outlier: 3.796A  pdb=" N   TYR A 666 " --> pdb=" O   LEU A 662 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLU A 667 " --> pdb=" O   GLY A 663 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   MET A 671 " --> pdb=" O   GLU A 667 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   PHE A 681 " --> pdb=" O   PHE A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 709
      removed outlier: 3.953A  pdb=" N   ARG A 701 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 724 through 746
      removed outlier: 3.599A  pdb=" N   ILE A 728 " --> pdb=" O   ALA A 724 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL A 737 " --> pdb=" O   ALA A 733 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   VAL A 738 " --> pdb=" O   ILE A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 759
    Processing helix  chain 'A' and resid 762 through 766
    Processing helix  chain 'A' and resid 797 through 802
      removed outlier: 3.769A  pdb=" N   LEU A 801 " --> pdb=" O   PRO A 797 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLY A 802 " --> pdb=" O   TYR A 798 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 797 through 802'
    Processing helix  chain 'A' and resid 825 through 856
    Processing helix  chain 'A' and resid 861 through 875
      removed outlier: 3.601A  pdb=" N   SER A 866 " --> pdb=" O   LYS A 862 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 108
    Processing helix  chain 'B' and resid 131 through 142
    Processing helix  chain 'B' and resid 205 through 220
    Processing helix  chain 'B' and resid 234 through 239
    Processing helix  chain 'B' and resid 264 through 273
    Processing helix  chain 'B' and resid 275 through 279
    Processing helix  chain 'B' and resid 284 through 293
    Processing helix  chain 'B' and resid 293 through 327
    Processing helix  chain 'B' and resid 331 through 339
    Processing helix  chain 'B' and resid 364 through 375
      removed outlier: 3.512A  pdb=" N   ILE B 373 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 409
    Processing helix  chain 'B' and resid 447 through 473
    Processing helix  chain 'B' and resid 474 through 488
    Processing helix  chain 'B' and resid 504 through 539
      removed outlier: 3.568A  pdb=" N   ALA B 508 " --> pdb=" O   THR B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 573
      removed outlier: 5.504A  pdb=" N   SER B 566 " --> pdb=" O   ASN B 562 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   CYS B 567 " --> pdb=" O   TYR B 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 638
      removed outlier: 3.879A  pdb=" N   LYS B 616 " --> pdb=" O   ILE B 612 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ALA B 617 " --> pdb=" O   MET B 613 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ILE B 618 " --> pdb=" O   GLY B 614 " (cutoff:3.500A)
      Proline residue:  B 628  - end of helix
      removed outlier: 3.525A  pdb=" N   GLY B 635 " --> pdb=" O   MET B 631 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 655
    Processing helix  chain 'B' and resid 662 through 681
      removed outlier: 3.797A  pdb=" N   TYR B 666 " --> pdb=" O   LEU B 662 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLU B 667 " --> pdb=" O   GLY B 663 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   MET B 671 " --> pdb=" O   GLU B 667 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   PHE B 681 " --> pdb=" O   PHE B 677 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 709
      removed outlier: 3.953A  pdb=" N   ARG B 701 " --> pdb=" O   ILE B 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 724 through 746
      removed outlier: 3.599A  pdb=" N   ILE B 728 " --> pdb=" O   ALA B 724 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL B 737 " --> pdb=" O   ALA B 733 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   VAL B 738 " --> pdb=" O   ILE B 734 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 749 through 759
    Processing helix  chain 'B' and resid 762 through 766
    Processing helix  chain 'B' and resid 797 through 802
      removed outlier: 3.770A  pdb=" N   LEU B 801 " --> pdb=" O   PRO B 797 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLY B 802 " --> pdb=" O   TYR B 798 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 797 through 802'
    Processing helix  chain 'B' and resid 825 through 856
    Processing helix  chain 'B' and resid 861 through 875
      removed outlier: 3.601A  pdb=" N   SER B 866 " --> pdb=" O   LYS B 862 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 116
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 348
      removed outlier: 3.627A  pdb=" N   TRP A 359 " --> pdb=" O   MET A 348 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 657 through 658
      removed outlier: 6.940A  pdb=" N   GLN A 657 " --> pdb=" O   ARG A 712 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 785
    Processing sheet with id=AA5, first strand: chain 'B' and resid 111 through 116
    Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 348
      removed outlier: 3.628A  pdb=" N   TRP B 359 " --> pdb=" O   MET B 348 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 657 through 658
      removed outlier: 6.942A  pdb=" N   GLN B 657 " --> pdb=" O   ARG B 712 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 782 through 785

    720 hydrogen bonds defined for protein.
    2106 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: 3.49

  Time building geometry restraints manager: 3.44 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: 3544
        1.34 -     1.46: 2910
        1.46 -     1.58: 5430
        1.58 -     1.69: 0
        1.69 -     1.81: 114
  Bond restraints: 11998
  Sorted by residual:
  bond pdb=" C   PRO A 763 "
       pdb=" N   PRO A 764 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.011 1.36e-02 5.41e+03 6.60e-01
  bond pdb=" C   PRO B 763 "
       pdb=" N   PRO B 764 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.011 1.36e-02 5.41e+03 6.32e-01
  bond pdb=" C   GLY B 387 "
       pdb=" O   GLY B 387 "
    ideal  model  delta    sigma   weight residual
    1.234  1.243 -0.010 1.21e-02 6.83e+03 6.18e-01
  bond pdb=" C   VAL B 384 "
       pdb=" O   VAL B 384 "
    ideal  model  delta    sigma   weight residual
    1.237  1.245 -0.009 1.13e-02 7.83e+03 5.83e-01
  bond pdb=" C   PHE A 382 "
       pdb=" O   PHE A 382 "
    ideal  model  delta    sigma   weight residual
    1.236  1.227  0.010 1.26e-02 6.30e+03 5.78e-01
  ... (remaining 11993 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 16137
        1.99 -     3.97: 111
        3.97 -     5.96: 14
        5.96 -     7.94: 2
        7.94 -     9.93: 2
  Bond angle restraints: 16266
  Sorted by residual:
  angle pdb=" CA  LEU A 662 "
        pdb=" CB  LEU A 662 "
        pdb=" CG  LEU A 662 "
      ideal   model   delta    sigma   weight residual
     116.30  126.23   -9.93 3.50e+00 8.16e-02 8.04e+00
  angle pdb=" CA  LEU B 662 "
        pdb=" CB  LEU B 662 "
        pdb=" CG  LEU B 662 "
      ideal   model   delta    sigma   weight residual
     116.30  126.20   -9.90 3.50e+00 8.16e-02 7.99e+00
  angle pdb=" N   PRO A 763 "
        pdb=" CA  PRO A 763 "
        pdb=" C   PRO A 763 "
      ideal   model   delta    sigma   weight residual
     110.70  114.03   -3.33 1.22e+00 6.72e-01 7.47e+00
  angle pdb=" N   PRO B 763 "
        pdb=" CA  PRO B 763 "
        pdb=" C   PRO B 763 "
      ideal   model   delta    sigma   weight residual
     110.70  114.02   -3.32 1.22e+00 6.72e-01 7.42e+00
  angle pdb=" C   PRO B 541 "
        pdb=" N   ARG B 542 "
        pdb=" CA  ARG B 542 "
      ideal   model   delta    sigma   weight residual
     125.02  129.32   -4.30 1.76e+00 3.23e-01 5.98e+00
  ... (remaining 16261 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.49: 6730
       17.49 -    34.97: 287
       34.97 -    52.45: 29
       52.45 -    69.94: 8
       69.94 -    87.42: 2
  Dihedral angle restraints: 7056
    sinusoidal: 2870
      harmonic: 4186
  Sorted by residual:
  dihedral pdb=" CA  LYS A 590 "
           pdb=" C   LYS A 590 "
           pdb=" N   TYR A 591 "
           pdb=" CA  TYR A 591 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.15  -16.85     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  LYS B 590 "
           pdb=" C   LYS B 590 "
           pdb=" N   TYR B 591 "
           pdb=" CA  TYR B 591 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.23  -16.77     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  GLU B 539 "
           pdb=" CB  GLU B 539 "
           pdb=" CG  GLU B 539 "
           pdb=" CD  GLU B 539 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.32  -57.32     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 7053 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1077
       0.028 -    0.055: 429
       0.055 -    0.083: 210
       0.083 -    0.110: 54
       0.110 -    0.138: 16
  Chirality restraints: 1786
  Sorted by residual:
  chirality pdb=" CB  ILE A 474 "
            pdb=" CA  ILE A 474 "
            pdb=" CG1 ILE A 474 "
            pdb=" CG2 ILE A 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CB  ILE B 474 "
            pdb=" CA  ILE B 474 "
            pdb=" CG1 ILE B 474 "
            pdb=" CG2 ILE B 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  ARG B 542 "
            pdb=" N   ARG B 542 "
            pdb=" C   ARG B 542 "
            pdb=" CB  ARG B 542 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.20e-01
  ... (remaining 1783 not shown)

  Planarity restraints: 2010
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 762 "    0.029 5.00e-02 4.00e+02   4.32e-02 2.99e+00
        pdb=" N   PRO B 763 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 763 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 763 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 762 "   -0.029 5.00e-02 4.00e+02   4.30e-02 2.96e+00
        pdb=" N   PRO A 763 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 763 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 763 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 818 "    0.024 5.00e-02 4.00e+02   3.62e-02 2.09e+00
        pdb=" N   PRO A 819 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 819 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 819 "    0.020 5.00e-02 4.00e+02
  ... (remaining 2007 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 136
        2.60 -     3.18: 10465
        3.18 -     3.75: 18594
        3.75 -     4.33: 24805
        4.33 -     4.90: 41172
  Nonbonded interactions: 95172
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B 349 "
            pdb=" SG  CYS B 807 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS B 338 "
            pdb=" SG  CYS B 365 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS B 352 "
            pdb=" SG  CYS B 356 "
     model   vdw
     2.031 3.760
  nonbonded pdb=" SG  CYS B 331 "
            pdb=" SG  CYS B 372 "
     model   vdw
     2.033 3.760
  nonbonded pdb=" O   CYS B 365 "
            pdb=" OG  SER B 368 "
     model   vdw
     2.211 3.040
  ... (remaining 95167 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.970
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     33.000
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
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   0.030  11998  Z= 0.188
  Angle     :  0.464   9.926  16266  Z= 0.249
  Chirality :  0.038   0.138   1786
  Planarity :  0.004   0.043   2010
  Dihedral  :  9.830  87.425   4348
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  5.25 %
    Favored  : 93.50 %
  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:  2.21 (0.23), residues: 1382
  helix:  2.62 (0.17), residues: 848
  sheet:  1.10 (0.58), residues: 64
  loop : -0.73 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 397 
 HIS   0.002   0.000   HIS A 249 
 PHE   0.014   0.001   PHE B 560 
 TYR   0.013   0.001   TYR A 580 
 ARG   0.002   0.000   ARG B 813 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 190
  time to evaluate  : 1.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  234 ASN cc_start: 0.8677 (m-40) cc_final: 0.8347 (p0)
REVERT: A  326 LEU cc_start: 0.8975 (mt) cc_final: 0.8741 (mt)
REVERT: A  385 PHE cc_start: 0.8610 (t80) cc_final: 0.8405 (t80)
REVERT: A  406 TYR cc_start: 0.8568 (t80) cc_final: 0.8228 (t80)
REVERT: A  409 ASP cc_start: 0.8854 (m-30) cc_final: 0.8369 (t0)
REVERT: A  461 PHE cc_start: 0.8306 (t80) cc_final: 0.7785 (m-10)
REVERT: A  524 LEU cc_start: 0.9711 (mm) cc_final: 0.9280 (tp)
REVERT: A  527 ILE cc_start: 0.9626 (mm) cc_final: 0.9386 (mt)
REVERT: A  544 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7156 (tp40)
REVERT: A  548 GLU cc_start: 0.8978 (tp30) cc_final: 0.8711 (mm-30)
REVERT: A  553 MET cc_start: 0.8156 (tpp) cc_final: 0.7720 (tpp)
REVERT: A  597 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8407 (t70)
REVERT: B  296 ILE cc_start: 0.7948 (mp) cc_final: 0.7609 (mm)
REVERT: B  327 ASP cc_start: 0.7904 (t0) cc_final: 0.7663 (t0)
REVERT: B  409 ASP cc_start: 0.8527 (m-30) cc_final: 0.8112 (t0)
REVERT: B  548 GLU cc_start: 0.9093 (tp30) cc_final: 0.8529 (tp30)
REVERT: B  749 ASP cc_start: 0.7937 (t70) cc_final: 0.7211 (t0)
REVERT: B  855 TYR cc_start: 0.7994 (t80) cc_final: 0.7739 (t80)
  outliers start: 16
  outliers final: 3
  residues processed: 204
  average time/residue: 1.1489
  time to fit residues: 257.5315
Evaluate side-chains
  121 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 116
  time to evaluate  : 1.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  544 GLN
Chi-restraints excluded: chain A residue  597 ASP
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  685 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    2.9990
   chunk 106 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 109 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 127 optimal weight:    3.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 308 GLN
A 351 GLN
** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 544 GLN
A 559 GLN
A 726 GLN
A 730 GLN
A 820 GLN
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 275 HIS
B 308 GLN
B 525 ASN
B 674 GLN
B 695 ASN
B 726 GLN
B 730 GLN
B 824 HIS
B 830 HIS

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071  11998  Z= 0.354
  Angle     :  0.646  13.357  16266  Z= 0.337
  Chirality :  0.044   0.193   1786
  Planarity :  0.005   0.049   2010
  Dihedral  :  4.885  53.775   1570
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 11.44 %
    Favored  : 85.89 %
  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:  1.71 (0.22), residues: 1382
  helix:  2.12 (0.17), residues: 874
  sheet:  1.60 (0.61), residues: 44
  loop : -0.87 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 829 
 HIS   0.005   0.001   HIS B 818 
 PHE   0.024   0.002   PHE B 462 
 TYR   0.013   0.002   TYR B 580 
 ARG   0.012   0.001   ARG A 219 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 123
  time to evaluate  : 1.430 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 HIS cc_start: 0.8576 (OUTLIER) cc_final: 0.8136 (t-90)
REVERT: A  234 ASN cc_start: 0.8814 (m-40) cc_final: 0.8490 (p0)
REVERT: A  242 TYR cc_start: 0.8616 (m-80) cc_final: 0.8393 (m-80)
REVERT: A  282 LYS cc_start: 0.6450 (OUTLIER) cc_final: 0.6159 (tptt)
REVERT: A  409 ASP cc_start: 0.8678 (m-30) cc_final: 0.8167 (t0)
REVERT: A  524 LEU cc_start: 0.9710 (mm) cc_final: 0.9460 (mt)
REVERT: A  527 ILE cc_start: 0.9652 (mm) cc_final: 0.9436 (mt)
REVERT: A  548 GLU cc_start: 0.9015 (tp30) cc_final: 0.8297 (tp30)
REVERT: A  553 MET cc_start: 0.8247 (tpp) cc_final: 0.7800 (tpp)
REVERT: A  597 ASP cc_start: 0.8739 (m-30) cc_final: 0.8514 (t70)
REVERT: A  750 MET cc_start: 0.9349 (ttp) cc_final: 0.9145 (ttm)
REVERT: B  242 TYR cc_start: 0.8561 (m-80) cc_final: 0.8287 (m-80)
REVERT: B  386 MET cc_start: 0.8276 (mmm) cc_final: 0.7636 (mmm)
REVERT: B  409 ASP cc_start: 0.8525 (m-30) cc_final: 0.8116 (t0)
REVERT: B  538 PHE cc_start: 0.8416 (t80) cc_final: 0.7834 (t80)
REVERT: B  548 GLU cc_start: 0.9136 (tp30) cc_final: 0.8532 (mp0)
REVERT: B  612 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8756 (mp)
REVERT: B  855 TYR cc_start: 0.8033 (t80) cc_final: 0.7799 (t80)
  outliers start: 34
  outliers final: 17
  residues processed: 151
  average time/residue: 1.2938
  time to fit residues: 213.6665
Evaluate side-chains
  125 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 1.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  282 LYS
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  625 VAL
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  859 ASP
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  612 ILE
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  859 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 105 optimal weight:    9.9990
   chunk 86 optimal weight:    0.2980
   chunk 35 optimal weight:    7.9990
   chunk 127 optimal weight:    2.9990
   chunk 137 optimal weight:    0.9990
   chunk 113 optimal weight:    3.9990
   chunk 126 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 102 optimal weight:    5.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 830 HIS
B 111 GLN
** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 674 GLN
B 695 ASN
B 730 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  11998  Z= 0.338
  Angle     :  0.623  13.955  16266  Z= 0.325
  Chirality :  0.043   0.209   1786
  Planarity :  0.005   0.046   2010
  Dihedral  :  4.580  55.953   1565
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 13.24 %
    Favored  : 83.62 %
  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:  1.57 (0.22), residues: 1382
  helix:  2.00 (0.17), residues: 878
  sheet:  1.27 (0.58), residues: 44
  loop : -0.89 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 829 
 HIS   0.005   0.001   HIS B 830 
 PHE   0.023   0.002   PHE B 462 
 TYR   0.016   0.001   TYR B 580 
 ARG   0.012   0.001   ARG A 219 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 112
  time to evaluate  : 1.793 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8014 (mp10) cc_final: 0.7781 (pm20)
REVERT: A   76 VAL cc_start: 0.9157 (t) cc_final: 0.8871 (p)
REVERT: A   94 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8140 (tp40)
REVERT: A  108 HIS cc_start: 0.8605 (OUTLIER) cc_final: 0.8176 (t-90)
REVERT: A  234 ASN cc_start: 0.8837 (m-40) cc_final: 0.8579 (p0)
REVERT: A  242 TYR cc_start: 0.8673 (m-80) cc_final: 0.8361 (m-80)
REVERT: A  348 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8655 (mmm)
REVERT: A  409 ASP cc_start: 0.8715 (m-30) cc_final: 0.8207 (t0)
REVERT: A  527 ILE cc_start: 0.9633 (mm) cc_final: 0.9393 (mt)
REVERT: A  548 GLU cc_start: 0.9055 (tp30) cc_final: 0.8354 (tp30)
REVERT: A  553 MET cc_start: 0.8271 (tpp) cc_final: 0.7822 (tpp)
REVERT: B  322 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8751 (mp)
REVERT: B  409 ASP cc_start: 0.8509 (m-30) cc_final: 0.8109 (t0)
REVERT: B  538 PHE cc_start: 0.8429 (t80) cc_final: 0.8128 (t80)
REVERT: B  548 GLU cc_start: 0.9102 (tp30) cc_final: 0.8543 (mp0)
REVERT: B  855 TYR cc_start: 0.8016 (t80) cc_final: 0.7798 (t80)
  outliers start: 40
  outliers final: 17
  residues processed: 143
  average time/residue: 1.2135
  time to fit residues: 190.2052
Evaluate side-chains
  120 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  859 ASP
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 ILE
Chi-restraints excluded: chain B residue  859 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 125 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 14 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 127 optimal weight:    2.9990
   chunk 135 optimal weight:    1.9990
   chunk 121 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 112 optimal weight:    3.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 559 GLN
** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 730 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.3761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  11998  Z= 0.388
  Angle     :  0.643  13.104  16266  Z= 0.335
  Chirality :  0.043   0.186   1786
  Planarity :  0.005   0.047   2010
  Dihedral  :  4.413  22.674   1562
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 13.64 %
    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:  1.41 (0.22), residues: 1382
  helix:  1.87 (0.17), residues: 876
  sheet:  0.88 (0.59), residues: 44
  loop : -0.90 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 829 
 HIS   0.005   0.001   HIS A 830 
 PHE   0.024   0.002   PHE B 462 
 TYR   0.018   0.001   TYR B 406 
 ARG   0.013   0.001   ARG B 219 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 105
  time to evaluate  : 1.503 
Fit side-chains
REVERT: A   76 VAL cc_start: 0.9158 (t) cc_final: 0.8920 (p)
REVERT: A   94 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8082 (tp40)
REVERT: A  108 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.8078 (t-90)
REVERT: A  234 ASN cc_start: 0.8883 (m-40) cc_final: 0.8655 (p0)
REVERT: A  282 LYS cc_start: 0.6596 (OUTLIER) cc_final: 0.6353 (tptt)
REVERT: A  409 ASP cc_start: 0.8768 (m-30) cc_final: 0.8269 (t0)
REVERT: A  527 ILE cc_start: 0.9655 (mm) cc_final: 0.9421 (mt)
REVERT: A  548 GLU cc_start: 0.9104 (tp30) cc_final: 0.8391 (tp30)
REVERT: A  553 MET cc_start: 0.8304 (tpp) cc_final: 0.7845 (tpp)
REVERT: B  269 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7721 (mt)
REVERT: B  409 ASP cc_start: 0.8470 (m-30) cc_final: 0.8070 (t0)
REVERT: B  458 SER cc_start: 0.8691 (m) cc_final: 0.8370 (p)
REVERT: B  507 MET cc_start: 0.4594 (pmt) cc_final: 0.4202 (pmm)
REVERT: B  538 PHE cc_start: 0.8390 (t80) cc_final: 0.8096 (t80)
REVERT: B  548 GLU cc_start: 0.9131 (tp30) cc_final: 0.8376 (tp30)
REVERT: B  742 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8195 (mtp)
REVERT: B  749 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.7828 (t0)
REVERT: B  855 TYR cc_start: 0.8057 (t80) cc_final: 0.7761 (t80)
  outliers start: 46
  outliers final: 28
  residues processed: 144
  average time/residue: 1.1009
  time to fit residues: 174.4165
Evaluate side-chains
  131 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 98
  time to evaluate  : 1.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  282 LYS
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  625 VAL
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  762 ILE
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  783 VAL
Chi-restraints excluded: chain A residue  859 ASP
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  464 ILE
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  687 LEU
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  742 MET
Chi-restraints excluded: chain B residue  749 ASP
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 ILE
Chi-restraints excluded: chain B residue  859 ASP
Chi-restraints excluded: chain B residue  863 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 100 optimal weight:   10.0000
   chunk 55 optimal weight:    0.8980
   chunk 115 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 121 optimal weight:    0.5980
   chunk 34 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 674 GLN
A 695 ASN
B 351 GLN
** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 674 GLN
B 695 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.3904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11998  Z= 0.238
  Angle     :  0.589  12.116  16266  Z= 0.304
  Chirality :  0.041   0.161   1786
  Planarity :  0.005   0.048   2010
  Dihedral  :  4.335  22.702   1562
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.75 %
    Favored  : 81.58 %
  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:  1.48 (0.22), residues: 1382
  helix:  2.00 (0.17), residues: 868
  sheet:  0.87 (0.60), residues: 44
  loop : -0.97 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 397 
 HIS   0.003   0.001   HIS A 249 
 PHE   0.025   0.002   PHE B 462 
 TYR   0.013   0.001   TYR B 580 
 ARG   0.015   0.001   ARG B 219 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 104
  time to evaluate  : 1.321 
Fit side-chains
REVERT: A   76 VAL cc_start: 0.9168 (t) cc_final: 0.8902 (p)
REVERT: A  108 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.8146 (t-90)
REVERT: A  234 ASN cc_start: 0.8900 (m-40) cc_final: 0.8658 (p0)
REVERT: A  282 LYS cc_start: 0.6514 (OUTLIER) cc_final: 0.6170 (tptt)
REVERT: A  386 MET cc_start: 0.8156 (tpp) cc_final: 0.7878 (mmm)
REVERT: A  409 ASP cc_start: 0.8750 (m-30) cc_final: 0.8260 (t0)
REVERT: A  527 ILE cc_start: 0.9653 (mm) cc_final: 0.9415 (mt)
REVERT: A  548 GLU cc_start: 0.9092 (tp30) cc_final: 0.8362 (tp30)
REVERT: A  553 MET cc_start: 0.8309 (tpp) cc_final: 0.7891 (tpp)
REVERT: A  742 MET cc_start: 0.8605 (mtt) cc_final: 0.8225 (mtm)
REVERT: B   53 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8290 (pm20)
REVERT: B  409 ASP cc_start: 0.8583 (m-30) cc_final: 0.8210 (t0)
REVERT: B  458 SER cc_start: 0.8726 (m) cc_final: 0.8417 (p)
REVERT: B  538 PHE cc_start: 0.8374 (t80) cc_final: 0.8037 (t80)
REVERT: B  548 GLU cc_start: 0.9098 (tp30) cc_final: 0.8499 (mp0)
REVERT: B  742 MET cc_start: 0.8533 (mpt) cc_final: 0.8202 (mtp)
REVERT: B  749 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.7793 (t0)
REVERT: B  754 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8987 (mp)
REVERT: B  855 TYR cc_start: 0.7999 (t80) cc_final: 0.7777 (t80)
  outliers start: 34
  outliers final: 19
  residues processed: 133
  average time/residue: 1.1397
  time to fit residues: 166.8462
Evaluate side-chains
  121 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 1.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  282 LYS
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  625 VAL
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   53 GLU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  749 ASP
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 121 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0970
   chunk 33 optimal weight:   10.0000
   chunk 135 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9990
   chunk 62 optimal weight:    0.2980
   chunk 11 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 130 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 401 GLN
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 401 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.3999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  11998  Z= 0.194
  Angle     :  0.581  11.643  16266  Z= 0.297
  Chirality :  0.040   0.148   1786
  Planarity :  0.005   0.050   2010
  Dihedral  :  4.228  22.606   1562
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.52 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.22), residues: 1382
  helix:  2.11 (0.17), residues: 866
  sheet:  0.24 (0.56), residues: 62
  loop : -0.96 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 397 
 HIS   0.003   0.001   HIS A 249 
 PHE   0.026   0.001   PHE B 462 
 TYR   0.015   0.001   TYR A 827 
 ARG   0.017   0.000   ARG B 219 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 110
  time to evaluate  : 1.431 
Fit side-chains
REVERT: A   73 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.5922 (m-80)
REVERT: A   76 VAL cc_start: 0.9182 (t) cc_final: 0.8922 (p)
REVERT: A  108 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.8186 (t-90)
REVERT: A  113 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6564 (pm20)
REVERT: A  234 ASN cc_start: 0.8906 (m-40) cc_final: 0.8650 (p0)
REVERT: A  282 LYS cc_start: 0.6415 (OUTLIER) cc_final: 0.6205 (tptm)
REVERT: A  386 MET cc_start: 0.8103 (tpp) cc_final: 0.7896 (mmm)
REVERT: A  409 ASP cc_start: 0.8754 (m-30) cc_final: 0.8254 (t0)
REVERT: A  527 ILE cc_start: 0.9653 (mm) cc_final: 0.9412 (mt)
REVERT: A  548 GLU cc_start: 0.9086 (tp30) cc_final: 0.8348 (tp30)
REVERT: A  553 MET cc_start: 0.8311 (tpp) cc_final: 0.7860 (tpp)
REVERT: A  668 TYR cc_start: 0.9126 (m-80) cc_final: 0.8809 (m-80)
REVERT: A  742 MET cc_start: 0.8574 (mtt) cc_final: 0.8175 (mtm)
REVERT: B  386 MET cc_start: 0.8153 (tpp) cc_final: 0.7757 (mmm)
REVERT: B  409 ASP cc_start: 0.8569 (m-30) cc_final: 0.8170 (t0)
REVERT: B  458 SER cc_start: 0.8723 (m) cc_final: 0.8414 (p)
REVERT: B  507 MET cc_start: 0.4499 (pmt) cc_final: 0.4154 (pmm)
REVERT: B  529 GLU cc_start: 0.8780 (tt0) cc_final: 0.8104 (pt0)
REVERT: B  538 PHE cc_start: 0.8210 (t80) cc_final: 0.7834 (t80)
REVERT: B  548 GLU cc_start: 0.9088 (tp30) cc_final: 0.8507 (mp0)
REVERT: B  595 GLU cc_start: 0.8068 (tt0) cc_final: 0.7829 (tt0)
REVERT: B  668 TYR cc_start: 0.9127 (m-80) cc_final: 0.8810 (m-80)
REVERT: B  742 MET cc_start: 0.8600 (mpt) cc_final: 0.8240 (mtp)
REVERT: B  749 ASP cc_start: 0.8832 (OUTLIER) cc_final: 0.7856 (t0)
REVERT: B  773 MET cc_start: 0.8157 (mmt) cc_final: 0.7955 (tpp)
  outliers start: 32
  outliers final: 21
  residues processed: 137
  average time/residue: 1.1204
  time to fit residues: 168.9765
Evaluate side-chains
  131 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 PHE
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  282 LYS
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  749 ASP
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 ILE
Chi-restraints excluded: chain B residue  863 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 114 optimal weight:    0.6980
   chunk 75 optimal weight:    5.9990
   chunk 134 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 275 HIS
A 674 GLN
A 695 ASN
B 674 GLN
B 695 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.4209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073  11998  Z= 0.400
  Angle     :  0.641  11.527  16266  Z= 0.336
  Chirality :  0.043   0.180   1786
  Planarity :  0.005   0.050   2010
  Dihedral  :  4.344  21.939   1562
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 15.28 %
    Favored  : 81.19 %
  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:  1.39 (0.22), residues: 1382
  helix:  1.91 (0.17), residues: 876
  sheet: -0.03 (0.54), residues: 62
  loop : -0.94 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 273 
 HIS   0.005   0.001   HIS B 830 
 PHE   0.026   0.002   PHE B 462 
 TYR   0.012   0.001   TYR A 406 
 ARG   0.015   0.001   ARG B 219 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 103
  time to evaluate  : 1.308 
Fit side-chains
REVERT: A   76 VAL cc_start: 0.9157 (t) cc_final: 0.8922 (p)
REVERT: A   94 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8152 (tp40)
REVERT: A  108 HIS cc_start: 0.8505 (OUTLIER) cc_final: 0.8167 (t-90)
REVERT: A  113 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6457 (pm20)
REVERT: A  142 MET cc_start: 0.8104 (mtp) cc_final: 0.7860 (mtm)
REVERT: A  409 ASP cc_start: 0.8761 (m-30) cc_final: 0.8294 (t0)
REVERT: A  527 ILE cc_start: 0.9664 (mm) cc_final: 0.9427 (mt)
REVERT: A  548 GLU cc_start: 0.9114 (tp30) cc_final: 0.8403 (tp30)
REVERT: A  553 MET cc_start: 0.8303 (tpp) cc_final: 0.7824 (tpp)
REVERT: A  749 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.7810 (t0)
REVERT: B  142 MET cc_start: 0.7987 (mtp) cc_final: 0.7769 (mtm)
REVERT: B  409 ASP cc_start: 0.8591 (m-30) cc_final: 0.8226 (t0)
REVERT: B  458 SER cc_start: 0.8696 (m) cc_final: 0.8382 (p)
REVERT: B  529 GLU cc_start: 0.8769 (tt0) cc_final: 0.8156 (pt0)
REVERT: B  538 PHE cc_start: 0.8245 (t80) cc_final: 0.7848 (t80)
REVERT: B  548 GLU cc_start: 0.9081 (tp30) cc_final: 0.8328 (tp30)
REVERT: B  742 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8211 (mtp)
REVERT: B  749 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.7957 (t0)
REVERT: B  750 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.9127 (ttm)
  outliers start: 45
  outliers final: 27
  residues processed: 140
  average time/residue: 1.1197
  time to fit residues: 172.5050
Evaluate side-chains
  136 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 103
  time to evaluate  : 1.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  625 VAL
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  331 CYS
Chi-restraints excluded: chain B residue  464 ILE
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  637 TYR
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  742 MET
Chi-restraints excluded: chain B residue  749 ASP
Chi-restraints excluded: chain B residue  750 MET
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 ILE
Chi-restraints excluded: chain B residue  863 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 80 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 12 optimal weight:    6.9990
   chunk 106 optimal weight:    2.9990
   chunk 122 optimal weight:    0.0670
   chunk 129 optimal weight:    0.7980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A 674 GLN
A 695 ASN
B  99 GLN
B 674 GLN
B 695 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  11998  Z= 0.182
  Angle     :  0.586  11.076  16266  Z= 0.300
  Chirality :  0.040   0.147   1786
  Planarity :  0.005   0.051   2010
  Dihedral  :  4.252  22.160   1562
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.38 %
    Favored  : 81.11 %
  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:  1.55 (0.22), residues: 1382
  helix:  2.11 (0.17), residues: 866
  sheet:  0.19 (0.55), residues: 62
  loop : -1.02 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 397 
 HIS   0.003   0.001   HIS A 249 
 PHE   0.028   0.001   PHE B 462 
 TYR   0.015   0.001   TYR A 406 
 ARG   0.012   0.001   ARG A 219 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 104
  time to evaluate  : 1.420 
Fit side-chains
REVERT: A   76 VAL cc_start: 0.9169 (t) cc_final: 0.8932 (p)
REVERT: A  108 HIS cc_start: 0.8477 (OUTLIER) cc_final: 0.8166 (t-90)
REVERT: A  113 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6444 (pm20)
REVERT: A  386 MET cc_start: 0.8222 (tpp) cc_final: 0.7842 (mmm)
REVERT: A  409 ASP cc_start: 0.8805 (m-30) cc_final: 0.8304 (t0)
REVERT: A  527 ILE cc_start: 0.9664 (mm) cc_final: 0.9420 (mt)
REVERT: A  548 GLU cc_start: 0.9088 (tp30) cc_final: 0.8356 (tp30)
REVERT: A  553 MET cc_start: 0.8291 (tpp) cc_final: 0.7853 (tpp)
REVERT: A  668 TYR cc_start: 0.9123 (m-80) cc_final: 0.8829 (m-80)
REVERT: A  742 MET cc_start: 0.8672 (mtt) cc_final: 0.8255 (mtm)
REVERT: A  749 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.7412 (t0)
REVERT: B  386 MET cc_start: 0.8158 (tpp) cc_final: 0.7734 (mmm)
REVERT: B  409 ASP cc_start: 0.8702 (m-30) cc_final: 0.8287 (t0)
REVERT: B  458 SER cc_start: 0.8718 (m) cc_final: 0.8459 (p)
REVERT: B  529 GLU cc_start: 0.8770 (tt0) cc_final: 0.8105 (pt0)
REVERT: B  538 PHE cc_start: 0.8307 (t80) cc_final: 0.7907 (t80)
REVERT: B  548 GLU cc_start: 0.9100 (tp30) cc_final: 0.8545 (mp0)
REVERT: B  668 TYR cc_start: 0.9124 (m-80) cc_final: 0.8820 (m-80)
REVERT: B  742 MET cc_start: 0.8596 (mpt) cc_final: 0.8251 (mtp)
REVERT: B  749 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.7746 (t0)
  outliers start: 32
  outliers final: 22
  residues processed: 128
  average time/residue: 1.1562
  time to fit residues: 163.5378
Evaluate side-chains
  127 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 1.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  625 VAL
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  637 TYR
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  749 ASP
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 117 optimal weight:    2.9990
   chunk 125 optimal weight:    0.9990
   chunk 129 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 54 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 113 optimal weight:    0.9980
   chunk 118 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0970
   chunk 132 optimal weight:    0.0170
   overall best weight:    0.5216

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.4321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11998  Z= 0.178
  Angle     :  0.581  11.332  16266  Z= 0.295
  Chirality :  0.040   0.155   1786
  Planarity :  0.005   0.069   2010
  Dihedral  :  4.201  22.943   1562
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.01 %
    Favored  : 80.72 %
  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 (0.22), residues: 1382
  helix:  2.14 (0.17), residues: 872
  sheet:  0.22 (0.55), residues: 62
  loop : -1.01 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 397 
 HIS   0.003   0.001   HIS A 249 
 PHE   0.029   0.001   PHE B 462 
 TYR   0.015   0.001   TYR A 406 
 ARG   0.018   0.000   ARG B 219 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 1.459 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 VAL cc_start: 0.9149 (t) cc_final: 0.8920 (p)
REVERT: A   96 ARG cc_start: 0.8356 (ptm160) cc_final: 0.7998 (ptp-110)
REVERT: A  108 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.8194 (t-90)
REVERT: A  113 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6477 (pm20)
REVERT: A  386 MET cc_start: 0.8195 (tpp) cc_final: 0.7807 (mmm)
REVERT: A  409 ASP cc_start: 0.8820 (m-30) cc_final: 0.8310 (t0)
REVERT: A  524 LEU cc_start: 0.9717 (mt) cc_final: 0.9409 (pp)
REVERT: A  527 ILE cc_start: 0.9669 (mm) cc_final: 0.9427 (mt)
REVERT: A  548 GLU cc_start: 0.9088 (tp30) cc_final: 0.8363 (tp30)
REVERT: A  553 MET cc_start: 0.8308 (tpp) cc_final: 0.7858 (tpp)
REVERT: A  668 TYR cc_start: 0.9123 (m-80) cc_final: 0.8840 (m-80)
REVERT: A  742 MET cc_start: 0.8723 (mtt) cc_final: 0.8238 (mtm)
REVERT: A  749 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.7320 (t0)
REVERT: B  142 MET cc_start: 0.7801 (mtp) cc_final: 0.7520 (mtm)
REVERT: B  386 MET cc_start: 0.8223 (tpp) cc_final: 0.7849 (mmm)
REVERT: B  409 ASP cc_start: 0.8694 (m-30) cc_final: 0.8270 (t0)
REVERT: B  458 SER cc_start: 0.8782 (m) cc_final: 0.8537 (p)
REVERT: B  524 LEU cc_start: 0.9679 (mt) cc_final: 0.9358 (pp)
REVERT: B  529 GLU cc_start: 0.8708 (tt0) cc_final: 0.8121 (pt0)
REVERT: B  538 PHE cc_start: 0.8345 (t80) cc_final: 0.7915 (t80)
REVERT: B  548 GLU cc_start: 0.9090 (tp30) cc_final: 0.8545 (mp0)
REVERT: B  668 TYR cc_start: 0.9124 (m-80) cc_final: 0.8811 (m-80)
REVERT: B  742 MET cc_start: 0.8578 (mpt) cc_final: 0.8163 (mtp)
REVERT: B  749 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.7837 (t0)
REVERT: B  773 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7845 (mmm)
  outliers start: 29
  outliers final: 20
  residues processed: 129
  average time/residue: 1.1256
  time to fit residues: 160.2628
Evaluate side-chains
  129 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  625 VAL
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  749 ASP
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 ILE
Chi-restraints excluded: chain B residue  773 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0070
   chunk 139 optimal weight:    0.9990
   chunk 128 optimal weight:    0.0980
   chunk 111 optimal weight:    0.0970
   chunk 11 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 118 optimal weight:    0.0030
   overall best weight:    0.2408

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.4365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  11998  Z= 0.155
  Angle     :  0.597  12.204  16266  Z= 0.297
  Chirality :  0.039   0.154   1786
  Planarity :  0.005   0.060   2010
  Dihedral  :  4.117  26.205   1562
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.63 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.22), residues: 1382
  helix:  2.20 (0.17), residues: 874
  sheet:  0.31 (0.56), residues: 62
  loop : -1.01 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 397 
 HIS   0.002   0.001   HIS A 249 
 PHE   0.029   0.001   PHE A 462 
 TYR   0.023   0.001   TYR B  77 
 ARG   0.015   0.000   ARG B 219 

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 1.418 
Fit side-chains
REVERT: A  108 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.8234 (t-90)
REVERT: A  386 MET cc_start: 0.8123 (tpp) cc_final: 0.7762 (mmm)
REVERT: A  409 ASP cc_start: 0.8805 (m-30) cc_final: 0.8267 (t0)
REVERT: A  524 LEU cc_start: 0.9679 (mt) cc_final: 0.9410 (pp)
REVERT: A  527 ILE cc_start: 0.9669 (mm) cc_final: 0.9424 (mt)
REVERT: A  548 GLU cc_start: 0.9080 (tp30) cc_final: 0.8351 (tp30)
REVERT: A  553 MET cc_start: 0.8252 (tpp) cc_final: 0.7823 (tpp)
REVERT: A  668 TYR cc_start: 0.9098 (m-80) cc_final: 0.8754 (m-80)
REVERT: A  742 MET cc_start: 0.8728 (mtt) cc_final: 0.8254 (mtm)
REVERT: B  142 MET cc_start: 0.7648 (mtp) cc_final: 0.7371 (mtm)
REVERT: B  386 MET cc_start: 0.8152 (tpp) cc_final: 0.7805 (mmm)
REVERT: B  409 ASP cc_start: 0.8673 (m-30) cc_final: 0.8208 (t0)
REVERT: B  458 SER cc_start: 0.8880 (m) cc_final: 0.8647 (p)
REVERT: B  524 LEU cc_start: 0.9657 (mt) cc_final: 0.9278 (pp)
REVERT: B  529 GLU cc_start: 0.8743 (tt0) cc_final: 0.8123 (pt0)
REVERT: B  538 PHE cc_start: 0.8372 (t80) cc_final: 0.7931 (t80)
REVERT: B  548 GLU cc_start: 0.9093 (tp30) cc_final: 0.8555 (mp0)
REVERT: B  668 TYR cc_start: 0.9113 (m-80) cc_final: 0.8768 (m-80)
REVERT: B  742 MET cc_start: 0.8665 (mpt) cc_final: 0.8208 (mtp)
REVERT: B  749 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.7742 (t0)
REVERT: B  773 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7691 (mmm)
  outliers start: 23
  outliers final: 18
  residues processed: 125
  average time/residue: 1.0610
  time to fit residues: 147.0435
Evaluate side-chains
  124 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 1.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  625 VAL
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  749 ASP
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  773 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 34 optimal weight:   20.0000
   chunk 102 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 111 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 114 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0470
   chunk 20 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
A 730 GLN
B 730 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.122165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.086661 restraints weight = 21743.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 2.99
r_work: 0.3089 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.4403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11998  Z= 0.191
  Angle     :  0.604  13.836  16266  Z= 0.300
  Chirality :  0.040   0.170   1786
  Planarity :  0.005   0.060   2010
  Dihedral  :  4.074  23.342   1562
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.55 %
    Favored  : 80.41 %
  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:  1.75 (0.22), residues: 1382
  helix:  2.25 (0.17), residues: 872
  sheet:  0.34 (0.56), residues: 62
  loop : -0.98 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 397 
 HIS   0.005   0.001   HIS A 108 
 PHE   0.027   0.001   PHE B 462 
 TYR   0.018   0.001   TYR B  77 
 ARG   0.015   0.000   ARG B 219 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3492.95 seconds
wall clock time: 64 minutes 48.21 seconds (3888.21 seconds total)