Starting phenix.real_space_refine
on Thu Mar 13 02:14:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k48_22661/03_2025/7k48_22661.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k48_22661/03_2025/7k48_22661.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k48_22661/03_2025/7k48_22661.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k48_22661/03_2025/7k48_22661.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k48_22661/03_2025/7k48_22661.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k48_22661/03_2025/7k48_22661.cif"
  }
  resolution = 3.6
  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=   0.069 sd=   0.926
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    5696      2.51       5
     N    1316      2.21       5
     O    1388      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8480
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1858
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1858
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 8, 'TRANS': 220}
    Chain: "E"
      Number of atoms: 262
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 262
          Classifications: {'peptide': 33}
          Link IDs: {'PTRANS': 1, 'TRANS': 31}
  Restraints were copied for chains:
    C, B, D, G, F, H
  Time building chain proxies: 4.41, per 1000 atoms: 0.52
  Number of scatterers: 8480
  At special positions: 0
  Unit cell: (123.552, 123.552, 72.864, 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    1388      8.00
     N    1316      7.00
     C    5696      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: 2.13
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2024

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      79.1% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 720 through 732
    Processing helix  chain 'A' and resid 732 through 751
    Processing helix  chain 'A' and resid 758 through 787
      removed outlier: 3.625A  pdb=" N   ASN A 763 " --> pdb=" O   GLU A 759 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   VAL A 764 " --> pdb=" O   GLU A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 794
      removed outlier: 3.901A  pdb=" N   ASP A 794 " --> pdb=" O   SER A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 811
    Processing helix  chain 'A' and resid 818 through 829
    Processing helix  chain 'A' and resid 830 through 835
    Processing helix  chain 'A' and resid 837 through 876
      removed outlier: 4.125A  pdb=" N   LYS A 842 " --> pdb=" O   PRO A 838 " (cutoff:3.500A)
      Proline residue:  A 852  - end of helix
    Processing helix  chain 'A' and resid 880 through 885
      removed outlier: 3.929A  pdb=" N   PHE A 884 " --> pdb=" O   PHE A 880 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 899
    Processing helix  chain 'A' and resid 907 through 915
      removed outlier: 3.599A  pdb=" N   VAL A 914 " --> pdb=" O   PRO A 910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 918 through 948
      Proline residue:  A 924  - end of helix
      removed outlier: 4.877A  pdb=" N   ASP A 943 " --> pdb=" O   ALA A 939 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   ALA A 944 " --> pdb=" O   ILE A 940 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   MET A 945 " --> pdb=" O   ILE A 941 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 732
    Processing helix  chain 'B' and resid 732 through 751
    Processing helix  chain 'B' and resid 758 through 787
      removed outlier: 3.624A  pdb=" N   ASN B 763 " --> pdb=" O   GLU B 759 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   VAL B 764 " --> pdb=" O   GLU B 760 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 789 through 794
      removed outlier: 3.901A  pdb=" N   ASP B 794 " --> pdb=" O   SER B 790 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 794 through 811
    Processing helix  chain 'B' and resid 818 through 829
    Processing helix  chain 'B' and resid 830 through 835
    Processing helix  chain 'B' and resid 837 through 876
      removed outlier: 4.126A  pdb=" N   LYS B 842 " --> pdb=" O   PRO B 838 " (cutoff:3.500A)
      Proline residue:  B 852  - end of helix
    Processing helix  chain 'B' and resid 880 through 885
      removed outlier: 3.928A  pdb=" N   PHE B 884 " --> pdb=" O   PHE B 880 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 887 through 899
    Processing helix  chain 'B' and resid 907 through 915
      removed outlier: 3.599A  pdb=" N   VAL B 914 " --> pdb=" O   PRO B 910 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 918 through 948
      Proline residue:  B 924  - end of helix
      removed outlier: 4.877A  pdb=" N   ASP B 943 " --> pdb=" O   ALA B 939 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   ALA B 944 " --> pdb=" O   ILE B 940 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   MET B 945 " --> pdb=" O   ILE B 941 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 721 through 732
    Processing helix  chain 'C' and resid 732 through 751
    Processing helix  chain 'C' and resid 758 through 787
      removed outlier: 3.624A  pdb=" N   ASN C 763 " --> pdb=" O   GLU C 759 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   VAL C 764 " --> pdb=" O   GLU C 760 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 789 through 794
      removed outlier: 3.901A  pdb=" N   ASP C 794 " --> pdb=" O   SER C 790 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 794 through 811
    Processing helix  chain 'C' and resid 818 through 829
    Processing helix  chain 'C' and resid 830 through 835
    Processing helix  chain 'C' and resid 837 through 876
      removed outlier: 4.125A  pdb=" N   LYS C 842 " --> pdb=" O   PRO C 838 " (cutoff:3.500A)
      Proline residue:  C 852  - end of helix
    Processing helix  chain 'C' and resid 880 through 885
      removed outlier: 3.928A  pdb=" N   PHE C 884 " --> pdb=" O   PHE C 880 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 887 through 899
    Processing helix  chain 'C' and resid 907 through 915
      removed outlier: 3.599A  pdb=" N   VAL C 914 " --> pdb=" O   PRO C 910 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 918 through 948
      Proline residue:  C 924  - end of helix
      removed outlier: 4.877A  pdb=" N   ASP C 943 " --> pdb=" O   ALA C 939 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   ALA C 944 " --> pdb=" O   ILE C 940 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   MET C 945 " --> pdb=" O   ILE C 941 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 721 through 732
    Processing helix  chain 'D' and resid 732 through 751
    Processing helix  chain 'D' and resid 758 through 787
      removed outlier: 3.624A  pdb=" N   ASN D 763 " --> pdb=" O   GLU D 759 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   VAL D 764 " --> pdb=" O   GLU D 760 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 789 through 794
      removed outlier: 3.902A  pdb=" N   ASP D 794 " --> pdb=" O   SER D 790 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 794 through 811
    Processing helix  chain 'D' and resid 818 through 829
    Processing helix  chain 'D' and resid 830 through 835
    Processing helix  chain 'D' and resid 837 through 876
      removed outlier: 4.125A  pdb=" N   LYS D 842 " --> pdb=" O   PRO D 838 " (cutoff:3.500A)
      Proline residue:  D 852  - end of helix
    Processing helix  chain 'D' and resid 880 through 885
      removed outlier: 3.929A  pdb=" N   PHE D 884 " --> pdb=" O   PHE D 880 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 887 through 899
    Processing helix  chain 'D' and resid 907 through 915
      removed outlier: 3.598A  pdb=" N   VAL D 914 " --> pdb=" O   PRO D 910 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 918 through 948
      Proline residue:  D 924  - end of helix
      removed outlier: 4.877A  pdb=" N   ASP D 943 " --> pdb=" O   ALA D 939 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   ALA D 944 " --> pdb=" O   ILE D 940 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   MET D 945 " --> pdb=" O   ILE D 941 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 17 through 20
    Processing helix  chain 'F' and resid 17 through 20
    Processing helix  chain 'G' and resid 17 through 20
    Processing helix  chain 'H' and resid 17 through 20
    Processing sheet with id=AA1, first strand: chain 'E' and resid 22 through 24
      removed outlier: 3.612A  pdb=" N   VAL E  23 " --> pdb=" O   LYS E  32 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 22 through 24
      removed outlier: 3.612A  pdb=" N   VAL F  23 " --> pdb=" O   LYS F  32 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'G' and resid 22 through 24
      removed outlier: 3.612A  pdb=" N   VAL G  23 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 24
      removed outlier: 3.613A  pdb=" N   VAL H  23 " --> pdb=" O   LYS H  32 " (cutoff:3.500A)

    573 hydrogen bonds defined for protein.
    1599 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: 2.31

  Time building geometry restraints manager: 2.52 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2475
        1.35 -     1.47: 2411
        1.47 -     1.60: 3690
        1.60 -     1.72: 0
        1.72 -     1.85: 132
  Bond restraints: 8708
  Sorted by residual:
  bond pdb=" C   ILE D 851 "
       pdb=" N   PRO D 852 "
    ideal  model  delta    sigma   weight residual
    1.336  1.391 -0.055 1.20e-02 6.94e+03 2.11e+01
  bond pdb=" C   ILE A 851 "
       pdb=" N   PRO A 852 "
    ideal  model  delta    sigma   weight residual
    1.336  1.391 -0.055 1.20e-02 6.94e+03 2.08e+01
  bond pdb=" C   ILE C 851 "
       pdb=" N   PRO C 852 "
    ideal  model  delta    sigma   weight residual
    1.336  1.390 -0.054 1.20e-02 6.94e+03 2.05e+01
  bond pdb=" C   ILE B 851 "
       pdb=" N   PRO B 852 "
    ideal  model  delta    sigma   weight residual
    1.336  1.390 -0.054 1.20e-02 6.94e+03 2.04e+01
  bond pdb=" C   HIS D 755 "
       pdb=" N   PRO D 756 "
    ideal  model  delta    sigma   weight residual
    1.334  1.385 -0.051 2.34e-02 1.83e+03 4.68e+00
  ... (remaining 8703 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 10959
        2.10 -     4.20: 717
        4.20 -     6.29: 96
        6.29 -     8.39: 24
        8.39 -    10.49: 20
  Bond angle restraints: 11816
  Sorted by residual:
  angle pdb=" CA  ARG H  29 "
        pdb=" CB  ARG H  29 "
        pdb=" CG  ARG H  29 "
      ideal   model   delta    sigma   weight residual
     114.10  124.34  -10.24 2.00e+00 2.50e-01 2.62e+01
  angle pdb=" CA  ARG F  29 "
        pdb=" CB  ARG F  29 "
        pdb=" CG  ARG F  29 "
      ideal   model   delta    sigma   weight residual
     114.10  124.34  -10.24 2.00e+00 2.50e-01 2.62e+01
  angle pdb=" CA  ARG E  29 "
        pdb=" CB  ARG E  29 "
        pdb=" CG  ARG E  29 "
      ideal   model   delta    sigma   weight residual
     114.10  124.30  -10.20 2.00e+00 2.50e-01 2.60e+01
  angle pdb=" CA  ARG G  29 "
        pdb=" CB  ARG G  29 "
        pdb=" CG  ARG G  29 "
      ideal   model   delta    sigma   weight residual
     114.10  124.26  -10.16 2.00e+00 2.50e-01 2.58e+01
  angle pdb=" C   VAL A 928 "
        pdb=" N   VAL A 929 "
        pdb=" CA  VAL A 929 "
      ideal   model   delta    sigma   weight residual
     121.02  115.09    5.93 1.51e+00 4.39e-01 1.54e+01
  ... (remaining 11811 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 4352
       17.90 -    35.81: 536
       35.81 -    53.71: 125
       53.71 -    71.62: 35
       71.62 -    89.52: 20
  Dihedral angle restraints: 5068
    sinusoidal: 1980
      harmonic: 3088
  Sorted by residual:
  dihedral pdb=" CA  VAL B 821 "
           pdb=" C   VAL B 821 "
           pdb=" N   LEU B 822 "
           pdb=" CA  LEU B 822 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.05   27.95     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  VAL D 821 "
           pdb=" C   VAL D 821 "
           pdb=" N   LEU D 822 "
           pdb=" CA  LEU D 822 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.12   27.88     0      5.00e+00 4.00e-02 3.11e+01
  dihedral pdb=" CA  VAL A 821 "
           pdb=" C   VAL A 821 "
           pdb=" N   LEU A 822 "
           pdb=" CA  LEU A 822 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.13   27.87     0      5.00e+00 4.00e-02 3.11e+01
  ... (remaining 5065 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 857
       0.051 -    0.101: 376
       0.101 -    0.152: 131
       0.152 -    0.203: 18
       0.203 -    0.253: 10
  Chirality restraints: 1392
  Sorted by residual:
  chirality pdb=" CG  LEU B 819 "
            pdb=" CB  LEU B 819 "
            pdb=" CD1 LEU B 819 "
            pdb=" CD2 LEU B 819 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CG  LEU A 819 "
            pdb=" CB  LEU A 819 "
            pdb=" CD1 LEU A 819 "
            pdb=" CD2 LEU A 819 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CG  LEU C 819 "
            pdb=" CB  LEU C 819 "
            pdb=" CD1 LEU C 819 "
            pdb=" CD2 LEU C 819 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.59e+00
  ... (remaining 1389 not shown)

  Planarity restraints: 1416
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 901 "    0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" CD  GLU B 901 "   -0.058 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 901 "    0.021 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 901 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU D 901 "   -0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" CD  GLU D 901 "    0.058 2.00e-02 2.50e+03
        pdb=" OE1 GLU D 901 "   -0.021 2.00e-02 2.50e+03
        pdb=" OE2 GLU D 901 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 901 "    0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" CD  GLU A 901 "   -0.058 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 901 "    0.021 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 901 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1413 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 103
        2.60 -     3.17: 7574
        3.17 -     3.75: 14053
        3.75 -     4.32: 17675
        4.32 -     4.90: 27897
  Nonbonded interactions: 67302
  Sorted by model distance:
  nonbonded pdb=" SG  CYS E   2 "
            pdb=" SG  CYS E  17 "
     model   vdw
     2.023 3.760
  nonbonded pdb=" SG  CYS E  16 "
            pdb=" SG  CYS E  31 "
     model   vdw
     2.023 3.760
  nonbonded pdb=" SG  CYS F  16 "
            pdb=" SG  CYS F  31 "
     model   vdw
     2.023 3.760
  nonbonded pdb=" SG  CYS G   2 "
            pdb=" SG  CYS G  17 "
     model   vdw
     2.023 3.760
  nonbonded pdb=" SG  CYS F   2 "
            pdb=" SG  CYS F  17 "
     model   vdw
     2.023 3.760
  ... (remaining 67297 not shown)

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

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:             1.530
  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:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.640
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
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      :  0.010   0.063   8708  Z= 0.613
  Angle     :  1.227  10.492  11816  Z= 0.674
  Chirality :  0.064   0.253   1392
  Planarity :  0.009   0.079   1416
  Dihedral  : 17.881  89.520   3044
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 14.47 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.52 (0.21), residues: 1032
  helix: -2.11 (0.15), residues: 712
  sheet:  None (None), residues: 0
  loop : -2.43 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.004   TRP G  30 
 HIS   0.002   0.001   HIS A 754 
 PHE   0.026   0.003   PHE C 772 
 TYR   0.022   0.004   TYR B 915 
 ARG   0.005   0.001   ARG E  26 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 325
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  866 TYR cc_start: 0.9143 (t80) cc_final: 0.8889 (t80)
REVERT: A  867 ILE cc_start: 0.9186 (pt) cc_final: 0.8892 (mp)
REVERT: A  874 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8565 (tm-30)
REVERT: A  898 MET cc_start: 0.8570 (tmm) cc_final: 0.7940 (tmm)
REVERT: B  866 TYR cc_start: 0.8958 (t80) cc_final: 0.8671 (t80)
REVERT: B  874 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8536 (tm-30)
REVERT: B  898 MET cc_start: 0.8657 (tmm) cc_final: 0.8040 (tmm)
REVERT: C  829 ARG cc_start: 0.8777 (mtp180) cc_final: 0.8446 (mtp180)
REVERT: C  898 MET cc_start: 0.8662 (tmm) cc_final: 0.7998 (tmm)
REVERT: D  748 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8908 (mm)
REVERT: D  759 GLU cc_start: 0.8308 (tp30) cc_final: 0.7604 (pm20)
REVERT: D  829 ARG cc_start: 0.8765 (mtp180) cc_final: 0.8426 (mtp180)
REVERT: D  898 MET cc_start: 0.8679 (tmm) cc_final: 0.8066 (tmm)
  outliers start: 32
  outliers final: 11
  residues processed: 337
  average time/residue: 0.2172
  time to fit residues: 96.6427
Evaluate side-chains
  275 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 263
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  764 VAL
Chi-restraints excluded: chain B residue  936 LEU
Chi-restraints excluded: chain C residue  745 LEU
Chi-restraints excluded: chain C residue  936 LEU
Chi-restraints excluded: chain D residue  745 LEU
Chi-restraints excluded: chain D residue  748 LEU
Chi-restraints excluded: chain D residue  770 LEU
Chi-restraints excluded: chain D residue  936 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 75 optimal weight:   20.0000
   chunk 42 optimal weight:    0.8980
   chunk 25 optimal weight:   20.0000
   chunk 51 optimal weight:    8.9990
   chunk 40 optimal weight:    0.8980
   chunk 78 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 47 optimal weight:   20.0000
   chunk 58 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 720 ASN
B 720 ASN
C 720 ASN
C 746 ASN
D 720 ASN
D 746 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.147435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.114883 restraints weight = 20369.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.118549 restraints weight = 8974.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.120738 restraints weight = 5389.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8708  Z= 0.200
  Angle     :  0.692  10.608  11816  Z= 0.355
  Chirality :  0.040   0.177   1392
  Planarity :  0.006   0.062   1416
  Dihedral  :  7.966  54.168   1130
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 19.47 %
    Favored  : 75.64 %
  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: -1.59 (0.24), residues: 1032
  helix: -0.74 (0.18), residues: 712
  sheet:  None (None), residues: 0
  loop : -1.44 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 903 
 HIS   0.002   0.001   HIS A 754 
 PHE   0.029   0.001   PHE B 831 
 TYR   0.018   0.002   TYR C 866 
 ARG   0.004   0.000   ARG A 783 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 279
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  748 LEU cc_start: 0.8991 (mm) cc_final: 0.8726 (mm)
REVERT: A  752 MET cc_start: 0.8546 (mtt) cc_final: 0.7243 (mmt)
REVERT: A  829 ARG cc_start: 0.8731 (mtp180) cc_final: 0.8322 (mtp85)
REVERT: A  840 MET cc_start: 0.6858 (mmm) cc_final: 0.6436 (mmp)
REVERT: A  866 TYR cc_start: 0.9050 (t80) cc_final: 0.8772 (t80)
REVERT: A  880 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8290 (p90)
REVERT: A  898 MET cc_start: 0.8704 (tmm) cc_final: 0.8169 (tmm)
REVERT: B  748 LEU cc_start: 0.9007 (mm) cc_final: 0.8649 (mm)
REVERT: B  752 MET cc_start: 0.8669 (mtt) cc_final: 0.7343 (mmt)
REVERT: B  829 ARG cc_start: 0.8743 (mtp180) cc_final: 0.8180 (mmm-85)
REVERT: B  866 TYR cc_start: 0.8896 (t80) cc_final: 0.8645 (t80)
REVERT: B  867 ILE cc_start: 0.9055 (pt) cc_final: 0.8855 (mp)
REVERT: B  874 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8416 (tm-30)
REVERT: B  880 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.8216 (p90)
REVERT: B  898 MET cc_start: 0.8659 (tmm) cc_final: 0.8057 (tmm)
REVERT: C  748 LEU cc_start: 0.9174 (mm) cc_final: 0.8910 (mm)
REVERT: C  750 MET cc_start: 0.8612 (tpt) cc_final: 0.8320 (tpt)
REVERT: C  829 ARG cc_start: 0.8760 (mtp180) cc_final: 0.8225 (mtp85)
REVERT: C  880 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7632 (p90)
REVERT: C  898 MET cc_start: 0.8678 (tmm) cc_final: 0.8119 (tmm)
REVERT: D  745 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9286 (mm)
REVERT: D  748 LEU cc_start: 0.9172 (mm) cc_final: 0.8962 (mm)
REVERT: D  750 MET cc_start: 0.8763 (tpt) cc_final: 0.8434 (tpt)
REVERT: D  829 ARG cc_start: 0.8715 (mtp180) cc_final: 0.8156 (mmm-85)
REVERT: D  866 TYR cc_start: 0.8897 (t80) cc_final: 0.8671 (t80)
REVERT: D  880 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8167 (p90)
REVERT: D  898 MET cc_start: 0.8677 (tmm) cc_final: 0.8154 (tmm)
  outliers start: 46
  outliers final: 23
  residues processed: 310
  average time/residue: 0.2194
  time to fit residues: 93.8155
Evaluate side-chains
  305 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 277
  time to evaluate  : 1.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  880 PHE
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue  929 VAL
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  764 VAL
Chi-restraints excluded: chain B residue  834 VAL
Chi-restraints excluded: chain B residue  880 PHE
Chi-restraints excluded: chain B residue  929 VAL
Chi-restraints excluded: chain B residue  935 ASN
Chi-restraints excluded: chain B residue  936 LEU
Chi-restraints excluded: chain C residue  722 MET
Chi-restraints excluded: chain C residue  745 LEU
Chi-restraints excluded: chain C residue  779 GLU
Chi-restraints excluded: chain C residue  834 VAL
Chi-restraints excluded: chain C residue  880 PHE
Chi-restraints excluded: chain C residue  929 VAL
Chi-restraints excluded: chain C residue  936 LEU
Chi-restraints excluded: chain D residue  722 MET
Chi-restraints excluded: chain D residue  745 LEU
Chi-restraints excluded: chain D residue  770 LEU
Chi-restraints excluded: chain D residue  834 VAL
Chi-restraints excluded: chain D residue  880 PHE
Chi-restraints excluded: chain D residue  929 VAL
Chi-restraints excluded: chain D residue  936 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 94 optimal weight:   20.0000
   chunk 21 optimal weight:    6.9990
   chunk 75 optimal weight:    9.9990
   chunk 9 optimal weight:    6.9990
   chunk 51 optimal weight:   40.0000
   chunk 18 optimal weight:    0.0570
   chunk 57 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 84 optimal weight:    6.9990
   chunk 91 optimal weight:   20.0000
   overall best weight:    3.3904

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

Flipped N/Q/H residues before XYZ refinement:
A 746 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.144341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.110858 restraints weight = 20723.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.114377 restraints weight = 8978.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.116541 restraints weight = 5398.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8708  Z= 0.269
  Angle     :  0.680   8.064  11816  Z= 0.352
  Chirality :  0.041   0.191   1392
  Planarity :  0.005   0.042   1416
  Dihedral  :  7.493  57.502   1128
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 24.68 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.97 (0.25), residues: 1032
  helix: -0.22 (0.18), residues: 708
  sheet:  None (None), residues: 0
  loop : -1.37 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP E  30 
 HIS   0.001   0.000   HIS D 755 
 PHE   0.028   0.002   PHE B 831 
 TYR   0.016   0.002   TYR A 915 
 ARG   0.004   0.001   ARG C 841 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  340 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 294
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  748 LEU cc_start: 0.9050 (mm) cc_final: 0.8792 (mm)
REVERT: A  829 ARG cc_start: 0.8796 (mtp180) cc_final: 0.8369 (mtp85)
REVERT: A  840 MET cc_start: 0.6961 (mmm) cc_final: 0.6719 (mmp)
REVERT: A  880 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8443 (p90)
REVERT: A  898 MET cc_start: 0.8805 (tmm) cc_final: 0.8205 (tmm)
REVERT: A  903 TRP cc_start: 0.8768 (p-90) cc_final: 0.7974 (p-90)
REVERT: B  748 LEU cc_start: 0.8964 (mm) cc_final: 0.8673 (mm)
REVERT: B  829 ARG cc_start: 0.8745 (mtp180) cc_final: 0.8136 (mmm-85)
REVERT: B  867 ILE cc_start: 0.9103 (pt) cc_final: 0.8901 (mp)
REVERT: B  874 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8435 (tm-30)
REVERT: B  880 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8379 (p90)
REVERT: C  724 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7808 (tp)
REVERT: C  748 LEU cc_start: 0.9181 (mm) cc_final: 0.8896 (mm)
REVERT: C  750 MET cc_start: 0.8587 (tpt) cc_final: 0.8323 (tpt)
REVERT: C  759 GLU cc_start: 0.8238 (tp30) cc_final: 0.7533 (pm20)
REVERT: C  829 ARG cc_start: 0.8803 (mtp180) cc_final: 0.8370 (mtp85)
REVERT: C  840 MET cc_start: 0.7073 (mmm) cc_final: 0.6856 (mmm)
REVERT: C  880 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8078 (p90)
REVERT: C  898 MET cc_start: 0.8778 (tmm) cc_final: 0.8215 (tmm)
REVERT: C  903 TRP cc_start: 0.8837 (p-90) cc_final: 0.7960 (p-90)
REVERT: D  748 LEU cc_start: 0.9256 (mm) cc_final: 0.9037 (mm)
REVERT: D  750 MET cc_start: 0.8786 (tpt) cc_final: 0.8507 (tpt)
REVERT: D  829 ARG cc_start: 0.8733 (mtp180) cc_final: 0.8315 (mtp85)
REVERT: D  840 MET cc_start: 0.6884 (mmm) cc_final: 0.6525 (mmp)
REVERT: D  880 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8325 (p90)
REVERT: D  898 MET cc_start: 0.8767 (tmm) cc_final: 0.8220 (tmm)
REVERT: D  903 TRP cc_start: 0.8778 (p-90) cc_final: 0.8002 (p-90)
  outliers start: 46
  outliers final: 30
  residues processed: 319
  average time/residue: 0.2023
  time to fit residues: 87.5409
Evaluate side-chains
  280 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 245
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  865 PHE
Chi-restraints excluded: chain A residue  880 PHE
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain B residue  733 SER
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  764 VAL
Chi-restraints excluded: chain B residue  834 VAL
Chi-restraints excluded: chain B residue  880 PHE
Chi-restraints excluded: chain B residue  929 VAL
Chi-restraints excluded: chain B residue  935 ASN
Chi-restraints excluded: chain B residue  936 LEU
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain C residue  740 THR
Chi-restraints excluded: chain C residue  834 VAL
Chi-restraints excluded: chain C residue  880 PHE
Chi-restraints excluded: chain C residue  929 VAL
Chi-restraints excluded: chain C residue  936 LEU
Chi-restraints excluded: chain D residue  722 MET
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  770 LEU
Chi-restraints excluded: chain D residue  821 VAL
Chi-restraints excluded: chain D residue  834 VAL
Chi-restraints excluded: chain D residue  871 MET
Chi-restraints excluded: chain D residue  880 PHE
Chi-restraints excluded: chain D residue  929 VAL
Chi-restraints excluded: chain D residue  936 LEU
Chi-restraints excluded: chain D residue  941 ILE
Chi-restraints excluded: chain E residue   33 TRP
Chi-restraints excluded: chain G residue   33 TRP
Chi-restraints excluded: chain H residue    6 PHE
Chi-restraints excluded: chain H residue   33 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 73 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0040
   chunk 26 optimal weight:   10.0000
   chunk 55 optimal weight:    0.1980
   chunk 19 optimal weight:    4.9990
   chunk 91 optimal weight:    8.9990
   chunk 17 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 75 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    0.4792

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

Flipped N/Q/H residues before XYZ refinement:
A 746 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.148917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.115612 restraints weight = 20490.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.119366 restraints weight = 8824.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.121581 restraints weight = 5285.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8708  Z= 0.190
  Angle     :  0.658   7.717  11816  Z= 0.337
  Chirality :  0.040   0.145   1392
  Planarity :  0.004   0.037   1416
  Dihedral  :  6.488  52.119   1124
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 25.64 %
    Favored  : 69.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.26), residues: 1032
  helix:  0.17 (0.18), residues: 720
  sheet:  None (None), residues: 0
  loop : -0.94 (0.39), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP G  30 
 HIS   0.002   0.001   HIS C 787 
 PHE   0.028   0.001   PHE C 802 
 TYR   0.009   0.002   TYR B 915 
 ARG   0.004   0.000   ARG B 841 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 279
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  748 LEU cc_start: 0.9021 (mm) cc_final: 0.8750 (mm)
REVERT: A  829 ARG cc_start: 0.8801 (mtp180) cc_final: 0.7902 (mmm-85)
REVERT: A  878 GLU cc_start: 0.7798 (pp20) cc_final: 0.7363 (pp20)
REVERT: A  903 TRP cc_start: 0.8679 (p-90) cc_final: 0.8205 (p-90)
REVERT: B  748 LEU cc_start: 0.8958 (mm) cc_final: 0.8653 (mm)
REVERT: B  829 ARG cc_start: 0.8781 (mtp180) cc_final: 0.7859 (mmm-85)
REVERT: B  874 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8391 (tm-30)
REVERT: B  880 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8414 (p90)
REVERT: B  905 MET cc_start: 0.8620 (mmm) cc_final: 0.8237 (mmm)
REVERT: C  724 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7693 (tp)
REVERT: C  748 LEU cc_start: 0.9231 (mm) cc_final: 0.8984 (mm)
REVERT: C  749 PHE cc_start: 0.8601 (t80) cc_final: 0.8341 (t80)
REVERT: C  829 ARG cc_start: 0.8781 (mtp180) cc_final: 0.8403 (mtp180)
REVERT: C  880 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8074 (p90)
REVERT: C  898 MET cc_start: 0.8671 (tmm) cc_final: 0.8135 (tmm)
REVERT: C  903 TRP cc_start: 0.8762 (p-90) cc_final: 0.7973 (p-90)
REVERT: D  749 PHE cc_start: 0.8501 (t80) cc_final: 0.8279 (t80)
REVERT: D  750 MET cc_start: 0.8708 (tpt) cc_final: 0.8396 (tpt)
REVERT: D  829 ARG cc_start: 0.8765 (mtp180) cc_final: 0.8387 (mtp180)
REVERT: D  880 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.8305 (p90)
REVERT: D  898 MET cc_start: 0.8702 (tmm) cc_final: 0.8157 (tmm)
REVERT: D  903 TRP cc_start: 0.8675 (p-90) cc_final: 0.7943 (p-90)
REVERT: D  905 MET cc_start: 0.8949 (mmp) cc_final: 0.8732 (mmm)
  outliers start: 47
  outliers final: 31
  residues processed: 304
  average time/residue: 0.2026
  time to fit residues: 83.3870
Evaluate side-chains
  292 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 257
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  865 PHE
Chi-restraints excluded: chain A residue  929 VAL
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  733 SER
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  764 VAL
Chi-restraints excluded: chain B residue  834 VAL
Chi-restraints excluded: chain B residue  865 PHE
Chi-restraints excluded: chain B residue  880 PHE
Chi-restraints excluded: chain B residue  929 VAL
Chi-restraints excluded: chain B residue  936 LEU
Chi-restraints excluded: chain C residue  722 MET
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain C residue  834 VAL
Chi-restraints excluded: chain C residue  880 PHE
Chi-restraints excluded: chain C residue  929 VAL
Chi-restraints excluded: chain C residue  936 LEU
Chi-restraints excluded: chain C residue  941 ILE
Chi-restraints excluded: chain D residue  722 MET
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  834 VAL
Chi-restraints excluded: chain D residue  880 PHE
Chi-restraints excluded: chain D residue  929 VAL
Chi-restraints excluded: chain D residue  936 LEU
Chi-restraints excluded: chain D residue  941 ILE
Chi-restraints excluded: chain E residue   33 TRP
Chi-restraints excluded: chain F residue   33 TRP
Chi-restraints excluded: chain G residue   33 TRP
Chi-restraints excluded: chain H residue    6 PHE
Chi-restraints excluded: chain H residue   33 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 68 optimal weight:    9.9990
   chunk 98 optimal weight:   30.0000
   chunk 47 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 44 optimal weight:   20.0000
   chunk 95 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 746 ASN
B 746 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.148644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.115262 restraints weight = 20388.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.118972 restraints weight = 8736.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.121180 restraints weight = 5203.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.3288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8708  Z= 0.194
  Angle     :  0.654   8.232  11816  Z= 0.337
  Chirality :  0.040   0.234   1392
  Planarity :  0.004   0.036   1416
  Dihedral  :  6.013  46.225   1122
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 27.13 %
    Favored  : 67.55 %
  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: -0.13 (0.26), residues: 1032
  helix:  0.39 (0.18), residues: 728
  sheet:  None (None), residues: 0
  loop : -1.03 (0.39), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP G  30 
 HIS   0.001   0.000   HIS D 787 
 PHE   0.030   0.001   PHE B 831 
 TYR   0.021   0.002   TYR D 866 
 ARG   0.005   0.000   ARG C 841 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 281
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  748 LEU cc_start: 0.9065 (mm) cc_final: 0.8833 (mm)
REVERT: A  829 ARG cc_start: 0.8780 (mtp180) cc_final: 0.8436 (mmm160)
REVERT: A  903 TRP cc_start: 0.8754 (p-90) cc_final: 0.8228 (p-90)
REVERT: B  748 LEU cc_start: 0.8982 (mm) cc_final: 0.8743 (mm)
REVERT: B  829 ARG cc_start: 0.8756 (mtp180) cc_final: 0.7745 (mmm-85)
REVERT: B  840 MET cc_start: 0.6591 (mmm) cc_final: 0.6272 (mmp)
REVERT: B  874 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8385 (tm-30)
REVERT: B  903 TRP cc_start: 0.8669 (p-90) cc_final: 0.7741 (p-90)
REVERT: B  905 MET cc_start: 0.8729 (mmm) cc_final: 0.8372 (mmm)
REVERT: C  724 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7669 (tp)
REVERT: C  748 LEU cc_start: 0.9216 (mm) cc_final: 0.8990 (mm)
REVERT: C  829 ARG cc_start: 0.8789 (mtp180) cc_final: 0.8010 (mmm-85)
REVERT: C  880 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8112 (p90)
REVERT: C  898 MET cc_start: 0.8746 (tmm) cc_final: 0.8195 (tmm)
REVERT: C  903 TRP cc_start: 0.8759 (p-90) cc_final: 0.7932 (p-90)
REVERT: D  724 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7763 (tp)
REVERT: D  749 PHE cc_start: 0.8568 (t80) cc_final: 0.8332 (t80)
REVERT: D  750 MET cc_start: 0.8669 (tpt) cc_final: 0.8203 (mmm)
REVERT: D  829 ARG cc_start: 0.8822 (mtp180) cc_final: 0.8428 (mtp180)
REVERT: D  898 MET cc_start: 0.8720 (tmm) cc_final: 0.8190 (tmm)
REVERT: D  903 TRP cc_start: 0.8749 (p-90) cc_final: 0.7954 (p-90)
REVERT: D  905 MET cc_start: 0.8930 (mmp) cc_final: 0.8723 (mmm)
  outliers start: 50
  outliers final: 30
  residues processed: 307
  average time/residue: 0.1956
  time to fit residues: 81.8765
Evaluate side-chains
  279 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 246
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  865 PHE
Chi-restraints excluded: chain A residue  929 VAL
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  770 LEU
Chi-restraints excluded: chain B residue  798 LEU
Chi-restraints excluded: chain B residue  834 VAL
Chi-restraints excluded: chain B residue  929 VAL
Chi-restraints excluded: chain B residue  931 PHE
Chi-restraints excluded: chain B residue  936 LEU
Chi-restraints excluded: chain C residue  722 MET
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain C residue  834 VAL
Chi-restraints excluded: chain C residue  857 VAL
Chi-restraints excluded: chain C residue  871 MET
Chi-restraints excluded: chain C residue  880 PHE
Chi-restraints excluded: chain C residue  929 VAL
Chi-restraints excluded: chain C residue  936 LEU
Chi-restraints excluded: chain D residue  722 MET
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  834 VAL
Chi-restraints excluded: chain D residue  871 MET
Chi-restraints excluded: chain D residue  936 LEU
Chi-restraints excluded: chain E residue   33 TRP
Chi-restraints excluded: chain F residue   33 TRP
Chi-restraints excluded: chain G residue   33 TRP
Chi-restraints excluded: chain H residue    6 PHE
Chi-restraints excluded: chain H residue   33 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 83 optimal weight:    0.6980
   chunk 14 optimal weight:    5.9990
   chunk 59 optimal weight:    6.9990
   chunk 89 optimal weight:    0.2980
   chunk 93 optimal weight:   20.0000
   chunk 87 optimal weight:    9.9990
   chunk 57 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 9 optimal weight:   20.0000
   overall best weight:    1.9986

-------------------------------------------------------------------------------
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 = 0.4181 r_free = 0.4181 target = 0.146679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.113840 restraints weight = 20650.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.117347 restraints weight = 8906.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.119401 restraints weight = 5362.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.3528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8708  Z= 0.225
  Angle     :  0.697  11.516  11816  Z= 0.359
  Chirality :  0.041   0.318   1392
  Planarity :  0.004   0.035   1416
  Dihedral  :  5.824  40.947   1120
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 16.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 29.04 %
    Favored  : 64.89 %
  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: -0.18 (0.26), residues: 1032
  helix:  0.35 (0.18), residues: 728
  sheet:  None (None), residues: 0
  loop : -1.05 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E  30 
 HIS   0.001   0.000   HIS C 787 
 PHE   0.034   0.001   PHE A 802 
 TYR   0.011   0.002   TYR A 915 
 ARG   0.005   0.000   ARG B 841 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 259
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  748 LEU cc_start: 0.9076 (mm) cc_final: 0.8844 (mm)
REVERT: A  829 ARG cc_start: 0.8772 (mtp180) cc_final: 0.8199 (mmm-85)
REVERT: A  903 TRP cc_start: 0.8774 (p-90) cc_final: 0.8095 (p-90)
REVERT: B  748 LEU cc_start: 0.9014 (mm) cc_final: 0.8772 (mm)
REVERT: B  829 ARG cc_start: 0.8732 (mtp180) cc_final: 0.7765 (mmm-85)
REVERT: B  840 MET cc_start: 0.6436 (mmm) cc_final: 0.6123 (mmp)
REVERT: B  874 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8324 (tm-30)
REVERT: B  903 TRP cc_start: 0.8815 (p-90) cc_final: 0.7968 (p-90)
REVERT: B  905 MET cc_start: 0.8821 (mmm) cc_final: 0.8496 (mmm)
REVERT: C  724 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7655 (tp)
REVERT: C  745 LEU cc_start: 0.9444 (mm) cc_final: 0.9167 (mm)
REVERT: C  748 LEU cc_start: 0.9233 (mm) cc_final: 0.8996 (mm)
REVERT: C  829 ARG cc_start: 0.8817 (mtp180) cc_final: 0.8062 (mmm-85)
REVERT: C  880 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8343 (p90)
REVERT: C  898 MET cc_start: 0.8734 (tmm) cc_final: 0.8216 (tmm)
REVERT: C  903 TRP cc_start: 0.8764 (p-90) cc_final: 0.7965 (p-90)
REVERT: D  724 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7740 (tp)
REVERT: D  745 LEU cc_start: 0.9465 (mm) cc_final: 0.9217 (mm)
REVERT: D  749 PHE cc_start: 0.8466 (t80) cc_final: 0.8190 (t80)
REVERT: D  750 MET cc_start: 0.8601 (tpt) cc_final: 0.8360 (mmm)
REVERT: D  759 GLU cc_start: 0.7891 (tp30) cc_final: 0.7490 (pm20)
REVERT: D  829 ARG cc_start: 0.8830 (mtp180) cc_final: 0.8091 (mmm-85)
REVERT: D  880 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7922 (p90)
REVERT: D  898 MET cc_start: 0.8747 (tmm) cc_final: 0.8244 (tmm)
REVERT: D  903 TRP cc_start: 0.8839 (p-90) cc_final: 0.8183 (p-90)
REVERT: G   31 CYS cc_start: 0.1442 (OUTLIER) cc_final: 0.1178 (p)
  outliers start: 57
  outliers final: 34
  residues processed: 295
  average time/residue: 0.1950
  time to fit residues: 78.6046
Evaluate side-chains
  285 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 246
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  880 PHE
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  733 SER
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  770 LEU
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  798 LEU
Chi-restraints excluded: chain B residue  834 VAL
Chi-restraints excluded: chain B residue  931 PHE
Chi-restraints excluded: chain B residue  936 LEU
Chi-restraints excluded: chain C residue  722 MET
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  834 VAL
Chi-restraints excluded: chain C residue  857 VAL
Chi-restraints excluded: chain C residue  870 ILE
Chi-restraints excluded: chain C residue  880 PHE
Chi-restraints excluded: chain C residue  936 LEU
Chi-restraints excluded: chain D residue  722 MET
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  834 VAL
Chi-restraints excluded: chain D residue  857 VAL
Chi-restraints excluded: chain D residue  880 PHE
Chi-restraints excluded: chain D residue  936 LEU
Chi-restraints excluded: chain E residue    9 CYS
Chi-restraints excluded: chain E residue   33 TRP
Chi-restraints excluded: chain F residue    9 CYS
Chi-restraints excluded: chain F residue   33 TRP
Chi-restraints excluded: chain G residue    9 CYS
Chi-restraints excluded: chain G residue   31 CYS
Chi-restraints excluded: chain G residue   33 TRP
Chi-restraints excluded: chain H residue    6 PHE
Chi-restraints excluded: chain H residue   33 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 99 optimal weight:    8.9990
   chunk 88 optimal weight:    8.9990
   chunk 97 optimal weight:    3.9990
   chunk 68 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 746 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.146785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.113639 restraints weight = 20815.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.117097 restraints weight = 9052.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.119209 restraints weight = 5490.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.3704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8708  Z= 0.231
  Angle     :  0.723  11.895  11816  Z= 0.366
  Chirality :  0.042   0.304   1392
  Planarity :  0.004   0.035   1416
  Dihedral  :  5.677  41.921   1120
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 16.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 31.06 %
    Favored  : 63.30 %
  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: -0.18 (0.26), residues: 1032
  helix:  0.34 (0.18), residues: 720
  sheet:  None (None), residues: 0
  loop : -1.01 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E  30 
 HIS   0.001   0.000   HIS D 787 
 PHE   0.029   0.001   PHE B 831 
 TYR   0.012   0.002   TYR B 915 
 ARG   0.005   0.000   ARG D 841 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 261
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  745 LEU cc_start: 0.9565 (mt) cc_final: 0.9350 (mt)
REVERT: A  748 LEU cc_start: 0.9127 (mm) cc_final: 0.8868 (mm)
REVERT: A  752 MET cc_start: 0.8386 (ptp) cc_final: 0.7090 (mmt)
REVERT: A  808 LEU cc_start: 0.8843 (mm) cc_final: 0.8556 (mm)
REVERT: A  829 ARG cc_start: 0.8810 (mtp180) cc_final: 0.8245 (mmm-85)
REVERT: A  898 MET cc_start: 0.8767 (tmm) cc_final: 0.8225 (tmm)
REVERT: B  745 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9293 (mt)
REVERT: B  748 LEU cc_start: 0.9049 (mm) cc_final: 0.8812 (mm)
REVERT: B  829 ARG cc_start: 0.8737 (mtp180) cc_final: 0.7790 (mmm-85)
REVERT: B  840 MET cc_start: 0.6402 (mmm) cc_final: 0.6083 (mmp)
REVERT: B  874 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8277 (tm-30)
REVERT: B  903 TRP cc_start: 0.8800 (p-90) cc_final: 0.7975 (p-90)
REVERT: B  905 MET cc_start: 0.8847 (mmm) cc_final: 0.8550 (mmm)
REVERT: C  724 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7760 (tp)
REVERT: C  745 LEU cc_start: 0.9414 (mm) cc_final: 0.9191 (mm)
REVERT: C  748 LEU cc_start: 0.9246 (mm) cc_final: 0.9005 (mm)
REVERT: C  829 ARG cc_start: 0.8828 (mtp180) cc_final: 0.8084 (mmm-85)
REVERT: C  898 MET cc_start: 0.8710 (tmm) cc_final: 0.8190 (tmm)
REVERT: C  903 TRP cc_start: 0.8807 (p-90) cc_final: 0.8022 (p-90)
REVERT: D  745 LEU cc_start: 0.9452 (mm) cc_final: 0.9172 (mm)
REVERT: D  749 PHE cc_start: 0.8499 (t80) cc_final: 0.8203 (t80)
REVERT: D  750 MET cc_start: 0.8650 (tpt) cc_final: 0.8437 (mmm)
REVERT: D  759 GLU cc_start: 0.7441 (tp30) cc_final: 0.7187 (pm20)
REVERT: D  829 ARG cc_start: 0.8842 (mtp180) cc_final: 0.8105 (mmm-85)
REVERT: D  903 TRP cc_start: 0.8830 (p-90) cc_final: 0.8069 (p-90)
REVERT: G   31 CYS cc_start: 0.1025 (OUTLIER) cc_final: 0.0732 (p)
  outliers start: 53
  outliers final: 31
  residues processed: 292
  average time/residue: 0.1918
  time to fit residues: 76.8250
Evaluate side-chains
  284 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 250
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  901 GLU
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  770 LEU
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  798 LEU
Chi-restraints excluded: chain B residue  834 VAL
Chi-restraints excluded: chain B residue  880 PHE
Chi-restraints excluded: chain B residue  931 PHE
Chi-restraints excluded: chain B residue  936 LEU
Chi-restraints excluded: chain C residue  722 MET
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain C residue  834 VAL
Chi-restraints excluded: chain C residue  870 ILE
Chi-restraints excluded: chain C residue  871 MET
Chi-restraints excluded: chain C residue  936 LEU
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  789 ILE
Chi-restraints excluded: chain D residue  834 VAL
Chi-restraints excluded: chain D residue  870 ILE
Chi-restraints excluded: chain D residue  936 LEU
Chi-restraints excluded: chain E residue    9 CYS
Chi-restraints excluded: chain E residue   33 TRP
Chi-restraints excluded: chain F residue    9 CYS
Chi-restraints excluded: chain F residue   33 TRP
Chi-restraints excluded: chain G residue    9 CYS
Chi-restraints excluded: chain G residue   31 CYS
Chi-restraints excluded: chain G residue   33 TRP
Chi-restraints excluded: chain H residue    6 PHE
Chi-restraints excluded: chain H residue   33 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 98 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 69 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 85 optimal weight:    0.1980
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 746 ASN
B 728 ASN
B 746 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.146837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.113145 restraints weight = 20808.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.116687 restraints weight = 9019.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.118690 restraints weight = 5436.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.3871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   8708  Z= 0.233
  Angle     :  0.731  11.898  11816  Z= 0.367
  Chirality :  0.042   0.298   1392
  Planarity :  0.004   0.037   1416
  Dihedral  :  5.522  42.443   1118
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 16.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 30.96 %
    Favored  : 63.72 %
  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: -0.08 (0.26), residues: 1032
  helix:  0.44 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop : -1.03 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  30 
 HIS   0.001   0.000   HIS D 787 
 PHE   0.040   0.001   PHE B 735 
 TYR   0.010   0.001   TYR A 915 
 ARG   0.006   0.000   ARG D 841 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 259
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  748 LEU cc_start: 0.9120 (mm) cc_final: 0.8889 (mm)
REVERT: A  752 MET cc_start: 0.8442 (ptp) cc_final: 0.7203 (mmt)
REVERT: A  808 LEU cc_start: 0.8830 (mm) cc_final: 0.8545 (mm)
REVERT: A  829 ARG cc_start: 0.8832 (mtp180) cc_final: 0.8275 (mmm-85)
REVERT: B  748 LEU cc_start: 0.9091 (mm) cc_final: 0.8706 (mm)
REVERT: B  752 MET cc_start: 0.8345 (ptp) cc_final: 0.7208 (tpt)
REVERT: B  829 ARG cc_start: 0.8754 (mtp180) cc_final: 0.7805 (mmm-85)
REVERT: B  840 MET cc_start: 0.6672 (mmm) cc_final: 0.6340 (mmp)
REVERT: B  874 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8016 (tm-30)
REVERT: B  903 TRP cc_start: 0.8852 (p-90) cc_final: 0.8112 (p-90)
REVERT: C  724 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7756 (mt)
REVERT: C  745 LEU cc_start: 0.9437 (mm) cc_final: 0.9185 (mm)
REVERT: C  748 LEU cc_start: 0.9255 (mm) cc_final: 0.8918 (mm)
REVERT: C  829 ARG cc_start: 0.8828 (mtp180) cc_final: 0.8079 (mmm-85)
REVERT: C  898 MET cc_start: 0.8788 (tmm) cc_final: 0.8312 (tmm)
REVERT: C  903 TRP cc_start: 0.8805 (p-90) cc_final: 0.8013 (p-90)
REVERT: D  724 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7724 (mt)
REVERT: D  745 LEU cc_start: 0.9423 (mm) cc_final: 0.9121 (mm)
REVERT: D  749 PHE cc_start: 0.8429 (t80) cc_final: 0.8067 (t80)
REVERT: D  759 GLU cc_start: 0.7512 (tp30) cc_final: 0.7129 (pm20)
REVERT: D  829 ARG cc_start: 0.8838 (mtp180) cc_final: 0.8090 (mmm-85)
REVERT: D  903 TRP cc_start: 0.8862 (p-90) cc_final: 0.8016 (p-90)
REVERT: G   31 CYS cc_start: 0.1079 (OUTLIER) cc_final: 0.0743 (p)
  outliers start: 50
  outliers final: 36
  residues processed: 289
  average time/residue: 0.2233
  time to fit residues: 88.2025
Evaluate side-chains
  297 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 258
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  880 PHE
Chi-restraints excluded: chain A residue  901 GLU
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  733 SER
Chi-restraints excluded: chain B residue  770 LEU
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  798 LEU
Chi-restraints excluded: chain B residue  834 VAL
Chi-restraints excluded: chain B residue  931 PHE
Chi-restraints excluded: chain B residue  936 LEU
Chi-restraints excluded: chain C residue  722 MET
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain C residue  728 ASN
Chi-restraints excluded: chain C residue  834 VAL
Chi-restraints excluded: chain C residue  857 VAL
Chi-restraints excluded: chain C residue  870 ILE
Chi-restraints excluded: chain C residue  871 MET
Chi-restraints excluded: chain C residue  936 LEU
Chi-restraints excluded: chain D residue  722 MET
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  789 ILE
Chi-restraints excluded: chain D residue  834 VAL
Chi-restraints excluded: chain D residue  857 VAL
Chi-restraints excluded: chain D residue  871 MET
Chi-restraints excluded: chain D residue  880 PHE
Chi-restraints excluded: chain D residue  936 LEU
Chi-restraints excluded: chain E residue    9 CYS
Chi-restraints excluded: chain E residue   33 TRP
Chi-restraints excluded: chain F residue   31 CYS
Chi-restraints excluded: chain F residue   33 TRP
Chi-restraints excluded: chain G residue    9 CYS
Chi-restraints excluded: chain G residue   31 CYS
Chi-restraints excluded: chain G residue   33 TRP
Chi-restraints excluded: chain H residue    6 PHE
Chi-restraints excluded: chain H residue   33 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:    8.9990
   chunk 47 optimal weight:    4.9990
   chunk 53 optimal weight:    8.9990
   chunk 26 optimal weight:    9.9990
   chunk 22 optimal weight:   20.0000
   chunk 91 optimal weight:   20.0000
   chunk 31 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 95 optimal weight:   30.0000
   chunk 64 optimal weight:    1.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
C 728 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.144294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.110315 restraints weight = 20814.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.113601 restraints weight = 9228.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.115612 restraints weight = 5651.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.3963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   8708  Z= 0.295
  Angle     :  0.774  11.965  11816  Z= 0.391
  Chirality :  0.044   0.355   1392
  Planarity :  0.004   0.040   1416
  Dihedral  :  5.512  43.412   1116
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 17.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 32.34 %
    Favored  : 62.45 %
  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: -0.23 (0.26), residues: 1032
  helix:  0.37 (0.19), residues: 728
  sheet:  None (None), residues: 0
  loop : -1.24 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G  30 
 HIS   0.001   0.000   HIS A 787 
 PHE   0.039   0.001   PHE B 735 
 TYR   0.025   0.002   TYR C 866 
 ARG   0.005   0.000   ARG B 841 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 257
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  748 LEU cc_start: 0.9097 (mm) cc_final: 0.8810 (mm)
REVERT: A  826 ARG cc_start: 0.8913 (mmm-85) cc_final: 0.8390 (mtm-85)
REVERT: A  829 ARG cc_start: 0.8832 (mtp180) cc_final: 0.8335 (mmm-85)
REVERT: A  898 MET cc_start: 0.8729 (tmm) cc_final: 0.8184 (tmm)
REVERT: B  748 LEU cc_start: 0.8981 (mm) cc_final: 0.8735 (mm)
REVERT: B  829 ARG cc_start: 0.8728 (mtp180) cc_final: 0.7737 (mmm-85)
REVERT: B  840 MET cc_start: 0.6704 (mmm) cc_final: 0.6363 (mmp)
REVERT: B  898 MET cc_start: 0.8784 (tmm) cc_final: 0.8268 (tmm)
REVERT: B  903 TRP cc_start: 0.8922 (p-90) cc_final: 0.8037 (p-90)
REVERT: C  724 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7738 (mt)
REVERT: C  745 LEU cc_start: 0.9455 (mm) cc_final: 0.9150 (mm)
REVERT: C  748 LEU cc_start: 0.9219 (mm) cc_final: 0.8967 (mm)
REVERT: C  829 ARG cc_start: 0.8841 (mtp180) cc_final: 0.8119 (mmm-85)
REVERT: C  903 TRP cc_start: 0.8911 (p-90) cc_final: 0.8176 (p-90)
REVERT: D  724 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7909 (mp)
REVERT: D  745 LEU cc_start: 0.9427 (mm) cc_final: 0.9163 (mm)
REVERT: D  749 PHE cc_start: 0.8547 (t80) cc_final: 0.8215 (t80)
REVERT: D  759 GLU cc_start: 0.7530 (tp30) cc_final: 0.7106 (pm20)
REVERT: D  831 PHE cc_start: 0.6611 (t80) cc_final: 0.6400 (t80)
REVERT: D  880 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.8141 (p90)
REVERT: D  903 TRP cc_start: 0.8941 (p-90) cc_final: 0.8146 (p-90)
REVERT: G   31 CYS cc_start: 0.1196 (OUTLIER) cc_final: 0.0834 (p)
  outliers start: 49
  outliers final: 32
  residues processed: 284
  average time/residue: 0.2050
  time to fit residues: 80.2827
Evaluate side-chains
  289 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 253
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  821 VAL
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  901 GLU
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  733 SER
Chi-restraints excluded: chain B residue  770 LEU
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  798 LEU
Chi-restraints excluded: chain B residue  834 VAL
Chi-restraints excluded: chain B residue  931 PHE
Chi-restraints excluded: chain B residue  936 LEU
Chi-restraints excluded: chain C residue  722 MET
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain C residue  728 ASN
Chi-restraints excluded: chain C residue  834 VAL
Chi-restraints excluded: chain C residue  857 VAL
Chi-restraints excluded: chain C residue  901 GLU
Chi-restraints excluded: chain C residue  936 LEU
Chi-restraints excluded: chain D residue  722 MET
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  789 ILE
Chi-restraints excluded: chain D residue  834 VAL
Chi-restraints excluded: chain D residue  857 VAL
Chi-restraints excluded: chain D residue  870 ILE
Chi-restraints excluded: chain D residue  871 MET
Chi-restraints excluded: chain D residue  880 PHE
Chi-restraints excluded: chain D residue  901 GLU
Chi-restraints excluded: chain D residue  936 LEU
Chi-restraints excluded: chain E residue   33 TRP
Chi-restraints excluded: chain F residue   31 CYS
Chi-restraints excluded: chain F residue   33 TRP
Chi-restraints excluded: chain G residue   31 CYS
Chi-restraints excluded: chain G residue   33 TRP
Chi-restraints excluded: chain H residue    6 PHE
Chi-restraints excluded: chain H residue   33 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 21 optimal weight:    7.9990
   chunk 86 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 94 optimal weight:    9.9990
   chunk 31 optimal weight:    0.0870
   overall best weight:    0.8960

-------------------------------------------------------------------------------
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 = 0.4203 r_free = 0.4203 target = 0.148296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.115299 restraints weight = 20502.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.118853 restraints weight = 8960.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.120938 restraints weight = 5380.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.4234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   8708  Z= 0.219
  Angle     :  0.796  13.501  11816  Z= 0.394
  Chirality :  0.043   0.334   1392
  Planarity :  0.004   0.042   1416
  Dihedral  :  5.586  44.337   1116
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 16.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 34.68 %
    Favored  : 61.70 %
  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: -0.20 (0.26), residues: 1032
  helix:  0.37 (0.19), residues: 728
  sheet:  None (None), residues: 0
  loop : -1.17 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP G  30 
 HIS   0.002   0.001   HIS C 755 
 PHE   0.045   0.001   PHE B 735 
 TYR   0.008   0.001   TYR C 785 
 ARG   0.006   0.000   ARG B 841 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 269
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  748 LEU cc_start: 0.9004 (mm) cc_final: 0.8781 (mm)
REVERT: A  752 MET cc_start: 0.8287 (ptp) cc_final: 0.7144 (mmt)
REVERT: A  808 LEU cc_start: 0.8882 (mm) cc_final: 0.8603 (mm)
REVERT: A  829 ARG cc_start: 0.8824 (mtp180) cc_final: 0.8138 (mmm-85)
REVERT: A  898 MET cc_start: 0.8685 (tmm) cc_final: 0.8138 (tmm)
REVERT: B  748 LEU cc_start: 0.9028 (mm) cc_final: 0.8742 (mm)
REVERT: B  829 ARG cc_start: 0.8794 (mtp180) cc_final: 0.8006 (mmm-85)
REVERT: B  840 MET cc_start: 0.6674 (mmm) cc_final: 0.6359 (mmp)
REVERT: B  903 TRP cc_start: 0.8856 (p-90) cc_final: 0.8161 (p-90)
REVERT: C  745 LEU cc_start: 0.9415 (mm) cc_final: 0.9152 (mm)
REVERT: C  748 LEU cc_start: 0.9150 (mm) cc_final: 0.8899 (mm)
REVERT: C  810 GLU cc_start: 0.7902 (tp30) cc_final: 0.7678 (tm-30)
REVERT: C  829 ARG cc_start: 0.8819 (mtp180) cc_final: 0.8075 (mmm-85)
REVERT: C  892 TYR cc_start: 0.8718 (t80) cc_final: 0.8148 (t80)
REVERT: C  898 MET cc_start: 0.8690 (tmm) cc_final: 0.8202 (tmm)
REVERT: D  724 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7750 (mt)
REVERT: D  749 PHE cc_start: 0.8493 (t80) cc_final: 0.8106 (t80)
REVERT: D  759 GLU cc_start: 0.7475 (tp30) cc_final: 0.6974 (pm20)
REVERT: D  829 ARG cc_start: 0.8656 (mtp180) cc_final: 0.8335 (mtp85)
REVERT: D  903 TRP cc_start: 0.8822 (p-90) cc_final: 0.8025 (p-90)
  outliers start: 34
  outliers final: 28
  residues processed: 284
  average time/residue: 0.1966
  time to fit residues: 75.9691
Evaluate side-chains
  283 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 254
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  880 PHE
Chi-restraints excluded: chain A residue  901 GLU
Chi-restraints excluded: chain B residue  733 SER
Chi-restraints excluded: chain B residue  770 LEU
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  834 VAL
Chi-restraints excluded: chain B residue  931 PHE
Chi-restraints excluded: chain B residue  936 LEU
Chi-restraints excluded: chain C residue  722 MET
Chi-restraints excluded: chain C residue  728 ASN
Chi-restraints excluded: chain C residue  752 MET
Chi-restraints excluded: chain C residue  834 VAL
Chi-restraints excluded: chain C residue  857 VAL
Chi-restraints excluded: chain C residue  901 GLU
Chi-restraints excluded: chain C residue  936 LEU
Chi-restraints excluded: chain D residue  722 MET
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  752 MET
Chi-restraints excluded: chain D residue  789 ILE
Chi-restraints excluded: chain D residue  834 VAL
Chi-restraints excluded: chain D residue  857 VAL
Chi-restraints excluded: chain D residue  936 LEU
Chi-restraints excluded: chain E residue   33 TRP
Chi-restraints excluded: chain F residue   33 TRP
Chi-restraints excluded: chain G residue   33 TRP
Chi-restraints excluded: chain H residue    6 PHE
Chi-restraints excluded: chain H residue   33 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 22 optimal weight:   20.0000
   chunk 41 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 96 optimal weight:   20.0000
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
C 728 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.146576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.113453 restraints weight = 20805.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.116724 restraints weight = 9439.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.118732 restraints weight = 5798.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.4290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   8708  Z= 0.259
  Angle     :  0.808  13.097  11816  Z= 0.406
  Chirality :  0.044   0.334   1392
  Planarity :  0.004   0.041   1416
  Dihedral  :  5.358  44.097   1114
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 17.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 35.96 %
    Favored  : 60.74 %
  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: -0.26 (0.26), residues: 1032
  helix:  0.32 (0.19), residues: 728
  sheet:  None (None), residues: 0
  loop : -1.18 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  30 
 HIS   0.001   0.000   HIS D 787 
 PHE   0.044   0.001   PHE B 735 
 TYR   0.011   0.002   TYR B 866 
 ARG   0.005   0.000   ARG B 841 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3441.85 seconds
wall clock time: 62 minutes 40.41 seconds (3760.41 seconds total)