Starting phenix.real_space_refine
on Tue Mar  3 20:15:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k48_22661/03_2026/7k48_22661.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k48_22661/03_2026/7k48_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k48_22661/03_2026/7k48_22661.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k48_22661/03_2026/7k48_22661.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k48_22661/03_2026/7k48_22661.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k48_22661/03_2026/7k48_22661.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.069 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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:
    B, C, D, F, G, H
  Time building chain proxies: 1.49, per 1000 atoms: 0.18
  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: 0.68
  Conformation dependent library (CDL) restraints added in 230.1 milliseconds
  

  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: 0.24
  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: 1.22

  Time building geometry restraints manager: 0.93 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  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:             1.110
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.030
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.490
-------------------------------------------------------------------------------
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= 0.437
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.005   0.001   ARG E  26 
 TYR   0.022   0.004   TYR B 915 
 PHE   0.026   0.003   PHE C 772 
 TRP   0.028   0.004   TRP G  30 
 HIS   0.002   0.001   HIS A 754 

Details of bonding type rmsd
  covalent geometry    : bond        0.00953 ( 8708)
  covalent geometry    : angle       1.22709 (11816)
  hydrogen bonds       : bond        0.12817 (  573)
  hydrogen bonds       : angle       7.15893 ( 1599)

*********************** 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  : 0.315 
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: 0.7941 (tmm)
REVERT: B  866 TYR cc_start: 0.8958 (t80) cc_final: 0.8671 (t80)
REVERT: B  874 GLN cc_start: 0.8792 (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: 0.0947
  time to fit residues: 42.6932
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  : 0.299 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    1.4186

-------------------------------------------------------------------------------
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 = 0.4171 r_free = 0.4171 target = 0.146767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.113677 restraints weight = 20460.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.117301 restraints weight = 8961.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.119433 restraints weight = 5387.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.120403 restraints weight = 4039.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.121224 restraints weight = 3524.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8708  Z= 0.163
  Angle     :  0.694  10.598  11816  Z= 0.358
  Chirality :  0.040   0.144   1392
  Planarity :  0.006   0.062   1416
  Dihedral  :  7.990  55.449   1130
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 14.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 20.21 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.24), residues: 1032
  helix: -0.73 (0.18), residues: 712
  sheet:  None (None), residues: 0
  loop : -1.44 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 841 
 TYR   0.018   0.002   TYR C 866 
 PHE   0.027   0.002   PHE B 831 
 TRP   0.014   0.001   TRP B 903 
 HIS   0.001   0.001   HIS A 754 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8708)
  covalent geometry    : angle       0.69397 (11816)
  hydrogen bonds       : bond        0.05208 (  573)
  hydrogen bonds       : angle       5.57359 ( 1599)

*********************** 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
  319 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 275
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  748 LEU cc_start: 0.8995 (mm) cc_final: 0.8730 (mm)
REVERT: A  752 MET cc_start: 0.8523 (mtt) cc_final: 0.7215 (mmt)
REVERT: A  829 ARG cc_start: 0.8718 (mtp180) cc_final: 0.8319 (mtp85)
REVERT: A  840 MET cc_start: 0.6911 (mmm) cc_final: 0.6479 (mmp)
REVERT: A  866 TYR cc_start: 0.9058 (t80) cc_final: 0.8768 (t80)
REVERT: A  880 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8299 (p90)
REVERT: A  898 MET cc_start: 0.8722 (tmm) cc_final: 0.8175 (tmm)
REVERT: B  748 LEU cc_start: 0.9011 (mm) cc_final: 0.8656 (mm)
REVERT: B  752 MET cc_start: 0.8659 (mtt) cc_final: 0.7323 (mmt)
REVERT: B  829 ARG cc_start: 0.8748 (mtp180) cc_final: 0.8202 (mmm-85)
REVERT: B  866 TYR cc_start: 0.8897 (t80) cc_final: 0.8640 (t80)
REVERT: B  874 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8411 (tm-30)
REVERT: B  880 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8207 (p90)
REVERT: B  898 MET cc_start: 0.8670 (tmm) cc_final: 0.8061 (tmm)
REVERT: C  748 LEU cc_start: 0.9169 (mm) cc_final: 0.8906 (mm)
REVERT: C  750 MET cc_start: 0.8587 (tpt) cc_final: 0.8306 (tpt)
REVERT: C  779 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.9088 (pt0)
REVERT: C  829 ARG cc_start: 0.8760 (mtp180) cc_final: 0.8224 (mtp85)
REVERT: C  880 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7598 (p90)
REVERT: C  898 MET cc_start: 0.8662 (tmm) cc_final: 0.8097 (tmm)
REVERT: D  745 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9282 (mm)
REVERT: D  748 LEU cc_start: 0.9174 (mm) cc_final: 0.8957 (mm)
REVERT: D  750 MET cc_start: 0.8732 (tpt) cc_final: 0.8383 (tpt)
REVERT: D  829 ARG cc_start: 0.8713 (mtp180) cc_final: 0.8158 (mmm-85)
REVERT: D  866 TYR cc_start: 0.8879 (t80) cc_final: 0.8678 (t80)
REVERT: D  880 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8172 (p90)
REVERT: D  898 MET cc_start: 0.8692 (tmm) cc_final: 0.8141 (tmm)
  outliers start: 44
  outliers final: 21
  residues processed: 303
  average time/residue: 0.0784
  time to fit residues: 33.3402
Evaluate side-chains
  299 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 272
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
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  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 29 optimal weight:   10.0000
   chunk 67 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 56 optimal weight:   10.0000
   chunk 91 optimal weight:   20.0000
   chunk 69 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   overall best weight:    2.6386

-------------------------------------------------------------------------------
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 = 0.4152 r_free = 0.4152 target = 0.145024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.111519 restraints weight = 20508.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.115061 restraints weight = 8891.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.117195 restraints weight = 5380.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.118119 restraints weight = 4057.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.118938 restraints weight = 3560.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   8708  Z= 0.173
  Angle     :  0.668   8.330  11816  Z= 0.345
  Chirality :  0.041   0.162   1392
  Planarity :  0.005   0.042   1416
  Dihedral  :  7.507  57.950   1128
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 23.40 %
    Favored  : 71.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.25), residues: 1032
  helix: -0.21 (0.18), residues: 712
  sheet:  None (None), residues: 0
  loop : -1.29 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 841 
 TYR   0.014   0.002   TYR A 915 
 PHE   0.027   0.001   PHE B 831 
 TRP   0.029   0.002   TRP E  30 
 HIS   0.001   0.000   HIS D 755 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 8708)
  covalent geometry    : angle       0.66750 (11816)
  hydrogen bonds       : bond        0.04764 (  573)
  hydrogen bonds       : angle       5.38818 ( 1599)

*********************** 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
  341 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 293
  time to evaluate  : 0.289 
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  748 LEU cc_start: 0.9040 (mm) cc_final: 0.8787 (mm)
REVERT: A  829 ARG cc_start: 0.8795 (mtp180) cc_final: 0.7924 (mmm-85)
REVERT: A  840 MET cc_start: 0.6981 (mmm) cc_final: 0.6745 (mmp)
REVERT: A  866 TYR cc_start: 0.9085 (t80) cc_final: 0.8844 (t80)
REVERT: A  880 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8348 (p90)
REVERT: A  898 MET cc_start: 0.8809 (tmm) cc_final: 0.8170 (tmm)
REVERT: A  903 TRP cc_start: 0.8750 (p-90) cc_final: 0.7914 (p-90)
REVERT: B  748 LEU cc_start: 0.8952 (mm) cc_final: 0.8657 (mm)
REVERT: B  829 ARG cc_start: 0.8753 (mtp180) cc_final: 0.8159 (mmm-85)
REVERT: B  874 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8407 (tm-30)
REVERT: B  880 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8362 (p90)
REVERT: C  724 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7791 (tp)
REVERT: C  745 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9318 (mm)
REVERT: C  748 LEU cc_start: 0.9168 (mm) cc_final: 0.8895 (mm)
REVERT: C  750 MET cc_start: 0.8577 (tpt) cc_final: 0.8275 (tpt)
REVERT: C  759 GLU cc_start: 0.8198 (tp30) cc_final: 0.7512 (pm20)
REVERT: C  826 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8470 (mmm-85)
REVERT: C  829 ARG cc_start: 0.8793 (mtp180) cc_final: 0.8138 (mmm-85)
REVERT: C  840 MET cc_start: 0.7104 (mmm) cc_final: 0.6895 (mmm)
REVERT: C  880 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8000 (p90)
REVERT: C  898 MET cc_start: 0.8716 (tmm) cc_final: 0.8150 (tmm)
REVERT: C  903 TRP cc_start: 0.8819 (p-90) cc_final: 0.7882 (p-90)
REVERT: D  748 LEU cc_start: 0.9249 (mm) cc_final: 0.9024 (mm)
REVERT: D  750 MET cc_start: 0.8745 (tpt) cc_final: 0.8475 (tpt)
REVERT: D  759 GLU cc_start: 0.8253 (tp30) cc_final: 0.7499 (pm20)
REVERT: D  829 ARG cc_start: 0.8745 (mtp180) cc_final: 0.8321 (mtp85)
REVERT: D  840 MET cc_start: 0.6886 (mmm) cc_final: 0.6549 (mmp)
REVERT: D  880 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8292 (p90)
REVERT: D  898 MET cc_start: 0.8754 (tmm) cc_final: 0.8194 (tmm)
  outliers start: 48
  outliers final: 27
  residues processed: 320
  average time/residue: 0.0866
  time to fit residues: 38.3865
Evaluate side-chains
  277 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 244
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
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  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 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  745 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 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  880 PHE
Chi-restraints excluded: chain D residue  929 VAL
Chi-restraints excluded: chain D residue  936 LEU
Chi-restraints excluded: chain E 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 92 optimal weight:    6.9990
   chunk 73 optimal weight:    9.9990
   chunk 81 optimal weight:    9.9990
   chunk 88 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0970
   chunk 68 optimal weight:   10.0000
   chunk 78 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 54 optimal weight:   10.0000
   chunk 47 optimal weight:    9.9990
   overall best weight:    4.0184

-------------------------------------------------------------------------------
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 = 0.4140 r_free = 0.4140 target = 0.143372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.109356 restraints weight = 21054.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.112721 restraints weight = 9221.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.114727 restraints weight = 5675.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.115644 restraints weight = 4346.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.116327 restraints weight = 3843.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8708  Z= 0.210
  Angle     :  0.690   7.252  11816  Z= 0.360
  Chirality :  0.041   0.166   1392
  Planarity :  0.005   0.036   1416
  Dihedral  :  6.980  56.339   1126
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 18.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 25.74 %
    Favored  : 68.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.25), residues: 1032
  helix:  0.10 (0.18), residues: 728
  sheet:  None (None), residues: 0
  loop : -1.19 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 841 
 TYR   0.018   0.002   TYR B 915 
 PHE   0.026   0.002   PHE C 802 
 TRP   0.015   0.002   TRP E  30 
 HIS   0.001   0.000   HIS D 755 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 8708)
  covalent geometry    : angle       0.69016 (11816)
  hydrogen bonds       : bond        0.04780 (  573)
  hydrogen bonds       : angle       5.42694 ( 1599)

*********************** 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
  313 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 257
  time to evaluate  : 0.306 
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: 0.9071 (mm) cc_final: 0.8546 (mm)
REVERT: A  829 ARG cc_start: 0.8782 (mtp180) cc_final: 0.7914 (mmm-85)
REVERT: A  840 MET cc_start: 0.7044 (mmm) cc_final: 0.6807 (mmp)
REVERT: A  866 TYR cc_start: 0.9093 (t80) cc_final: 0.8873 (t80)
REVERT: A  874 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8395 (tm-30)
REVERT: A  880 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8458 (p90)
REVERT: A  898 MET cc_start: 0.8803 (tmm) cc_final: 0.8217 (tmm)
REVERT: A  903 TRP cc_start: 0.8825 (p-90) cc_final: 0.8275 (p-90)
REVERT: B  748 LEU cc_start: 0.9014 (mm) cc_final: 0.8736 (mm)
REVERT: B  840 MET cc_start: 0.7027 (mmm) cc_final: 0.6801 (mmm)
REVERT: B  841 ARG cc_start: 0.7482 (ttp80) cc_final: 0.7239 (ttp80)
REVERT: B  874 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8413 (tm-30)
REVERT: B  880 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8431 (p90)
REVERT: B  901 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8175 (pp20)
REVERT: B  903 TRP cc_start: 0.8848 (p-90) cc_final: 0.7991 (p-90)
REVERT: C  745 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9226 (mm)
REVERT: C  748 LEU cc_start: 0.9210 (mm) cc_final: 0.8988 (mm)
REVERT: C  750 MET cc_start: 0.8450 (tpt) cc_final: 0.8178 (tpt)
REVERT: C  826 ARG cc_start: 0.8711 (mmm-85) cc_final: 0.8510 (mmm-85)
REVERT: C  829 ARG cc_start: 0.8792 (mtp180) cc_final: 0.8160 (mmm-85)
REVERT: C  840 MET cc_start: 0.6925 (mmm) cc_final: 0.6564 (mmp)
REVERT: C  880 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8241 (p90)
REVERT: C  898 MET cc_start: 0.8740 (tmm) cc_final: 0.8227 (tmm)
REVERT: C  903 TRP cc_start: 0.8903 (p-90) cc_final: 0.8019 (p-90)
REVERT: D  750 MET cc_start: 0.8709 (tpt) cc_final: 0.8388 (tpt)
REVERT: D  829 ARG cc_start: 0.8742 (mtp180) cc_final: 0.8357 (mtp180)
REVERT: D  840 MET cc_start: 0.6965 (mmm) cc_final: 0.6534 (mmp)
REVERT: D  880 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8405 (p90)
REVERT: D  898 MET cc_start: 0.8766 (tmm) cc_final: 0.8260 (tmm)
REVERT: D  903 TRP cc_start: 0.8804 (p-90) cc_final: 0.7918 (p-90)
  outliers start: 56
  outliers final: 31
  residues processed: 287
  average time/residue: 0.0829
  time to fit residues: 33.2595
Evaluate side-chains
  283 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 247
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
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  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  764 VAL
Chi-restraints excluded: chain B residue  770 LEU
Chi-restraints excluded: chain B residue  834 VAL
Chi-restraints excluded: chain B residue  880 PHE
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  724 LEU
Chi-restraints excluded: chain C residue  745 LEU
Chi-restraints excluded: chain C residue  834 VAL
Chi-restraints excluded: chain C residue  871 MET
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  740 THR
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 54 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 22 optimal weight:   20.0000
   chunk 31 optimal weight:    5.9990
   chunk 51 optimal weight:    8.9990
   chunk 14 optimal weight:    0.8980
   chunk 96 optimal weight:    9.9990
   chunk 9 optimal weight:   20.0000
   chunk 45 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
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 = 0.4147 r_free = 0.4147 target = 0.143959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.110074 restraints weight = 20746.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.113464 restraints weight = 9175.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.115520 restraints weight = 5643.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.116642 restraints weight = 4299.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.117228 restraints weight = 3737.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.3134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8708  Z= 0.185
  Angle     :  0.675   6.789  11816  Z= 0.350
  Chirality :  0.041   0.195   1392
  Planarity :  0.004   0.033   1416
  Dihedral  :  6.669  46.347   1126
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 17.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  6.60 %
    Allowed  : 26.91 %
    Favored  : 66.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.25), residues: 1032
  helix:  0.25 (0.18), residues: 728
  sheet:  None (None), residues: 0
  loop : -1.09 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 841 
 TYR   0.015   0.002   TYR B 915 
 PHE   0.030   0.001   PHE B 831 
 TRP   0.013   0.001   TRP E  30 
 HIS   0.001   0.000   HIS D 755 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 8708)
  covalent geometry    : angle       0.67542 (11816)
  hydrogen bonds       : bond        0.04740 (  573)
  hydrogen bonds       : angle       5.34127 ( 1599)

*********************** 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
  322 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 260
  time to evaluate  : 0.225 
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: 0.8992 (mm) cc_final: 0.8686 (mm)
REVERT: A  808 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7940 (mm)
REVERT: A  829 ARG cc_start: 0.8797 (mtp180) cc_final: 0.8214 (mmm-85)
REVERT: A  903 TRP cc_start: 0.8846 (p-90) cc_final: 0.8196 (p-90)
REVERT: B  748 LEU cc_start: 0.9057 (mm) cc_final: 0.8820 (mm)
REVERT: B  808 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8001 (mm)
REVERT: B  829 ARG cc_start: 0.8740 (mtp180) cc_final: 0.8144 (mmm-85)
REVERT: B  840 MET cc_start: 0.6735 (mmm) cc_final: 0.6319 (mmp)
REVERT: B  874 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8396 (tm-30)
REVERT: B  880 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8517 (p90)
REVERT: B  903 TRP cc_start: 0.8859 (p-90) cc_final: 0.7971 (p-90)
REVERT: C  724 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7722 (tp)
REVERT: C  745 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9110 (mm)
REVERT: C  748 LEU cc_start: 0.9198 (mm) cc_final: 0.8994 (mm)
REVERT: C  750 MET cc_start: 0.8407 (tpt) cc_final: 0.8114 (tpt)
REVERT: C  808 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7966 (mm)
REVERT: C  826 ARG cc_start: 0.8713 (mmm-85) cc_final: 0.8506 (mmm-85)
REVERT: C  829 ARG cc_start: 0.8804 (mtp180) cc_final: 0.8162 (mmm-85)
REVERT: C  840 MET cc_start: 0.6836 (mmm) cc_final: 0.6448 (mmp)
REVERT: C  880 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8396 (p90)
REVERT: C  898 MET cc_start: 0.8733 (tmm) cc_final: 0.8231 (tmm)
REVERT: C  903 TRP cc_start: 0.8880 (p-90) cc_final: 0.8006 (p-90)
REVERT: D  748 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8911 (mm)
REVERT: D  750 MET cc_start: 0.8640 (tpt) cc_final: 0.8413 (tpt)
REVERT: D  829 ARG cc_start: 0.8754 (mtp180) cc_final: 0.8373 (mtp180)
REVERT: D  880 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8493 (p90)
REVERT: D  898 MET cc_start: 0.8758 (tmm) cc_final: 0.8268 (tmm)
REVERT: D  903 TRP cc_start: 0.8837 (p-90) cc_final: 0.7964 (p-90)
REVERT: F   31 CYS cc_start: 0.2064 (OUTLIER) cc_final: 0.1819 (p)
REVERT: G   31 CYS cc_start: 0.1390 (OUTLIER) cc_final: 0.1063 (p)
  outliers start: 62
  outliers final: 27
  residues processed: 296
  average time/residue: 0.0844
  time to fit residues: 34.6409
Evaluate side-chains
  289 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 251
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  808 LEU
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  764 VAL
Chi-restraints excluded: chain B residue  770 LEU
Chi-restraints excluded: chain B residue  808 LEU
Chi-restraints excluded: chain B residue  834 VAL
Chi-restraints excluded: chain B residue  880 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  745 LEU
Chi-restraints excluded: chain C residue  808 LEU
Chi-restraints excluded: chain C residue  834 VAL
Chi-restraints excluded: chain C residue  871 MET
Chi-restraints excluded: chain C residue  880 PHE
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  740 THR
Chi-restraints excluded: chain D residue  748 LEU
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  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   31 CYS
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 46 optimal weight:    0.7980
   chunk 2 optimal weight:   10.0000
   chunk 83 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0970
   chunk 77 optimal weight:   10.0000
   chunk 28 optimal weight:    0.3980
   chunk 14 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
C 746 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 = 0.146649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.112904 restraints weight = 20521.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.116430 restraints weight = 9030.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.118513 restraints weight = 5507.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.119497 restraints weight = 4175.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.119814 restraints weight = 3669.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8708  Z= 0.147
  Angle     :  0.678   7.463  11816  Z= 0.350
  Chirality :  0.040   0.157   1392
  Planarity :  0.004   0.035   1416
  Dihedral  :  5.903  49.413   1119
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 15.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 28.51 %
    Favored  : 65.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.26), residues: 1032
  helix:  0.38 (0.18), residues: 728
  sheet:  None (None), residues: 0
  loop : -0.98 (0.39), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 841 
 TYR   0.012   0.002   TYR A 866 
 PHE   0.034   0.001   PHE B 802 
 TRP   0.012   0.001   TRP E  30 
 HIS   0.002   0.001   HIS C 787 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8708)
  covalent geometry    : angle       0.67754 (11816)
  hydrogen bonds       : bond        0.04664 (  573)
  hydrogen bonds       : angle       5.12302 ( 1599)

*********************** 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
  324 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 269
  time to evaluate  : 0.217 
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: 0.8970 (mm) cc_final: 0.8709 (mm)
REVERT: A  779 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8809 (pt0)
REVERT: A  829 ARG cc_start: 0.8805 (mtp180) cc_final: 0.8236 (mmm-85)
REVERT: A  840 MET cc_start: 0.6373 (mmp) cc_final: 0.6154 (mmp)
REVERT: A  903 TRP cc_start: 0.8766 (p-90) cc_final: 0.7972 (p-90)
REVERT: B  748 LEU cc_start: 0.9065 (mm) cc_final: 0.8830 (mm)
REVERT: B  829 ARG cc_start: 0.8795 (mtp180) cc_final: 0.7914 (mmm-85)
REVERT: B  874 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8326 (tm-30)
REVERT: B  903 TRP cc_start: 0.8821 (p-90) cc_final: 0.7937 (p-90)
REVERT: C  724 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7643 (tp)
REVERT: C  745 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9026 (mm)
REVERT: C  748 LEU cc_start: 0.9204 (mm) cc_final: 0.8994 (mm)
REVERT: C  750 MET cc_start: 0.8454 (tpt) cc_final: 0.8154 (tpt)
REVERT: C  829 ARG cc_start: 0.8816 (mtp180) cc_final: 0.8412 (mtp85)
REVERT: C  840 MET cc_start: 0.7018 (mmm) cc_final: 0.6586 (mmp)
REVERT: C  880 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8383 (p90)
REVERT: C  898 MET cc_start: 0.8694 (tmm) cc_final: 0.8185 (tmm)
REVERT: C  903 TRP cc_start: 0.8810 (p-90) cc_final: 0.7983 (p-90)
REVERT: D  724 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7738 (tp)
REVERT: D  749 PHE cc_start: 0.8404 (t80) cc_final: 0.8161 (t80)
REVERT: D  750 MET cc_start: 0.8697 (tpt) cc_final: 0.8459 (tpt)
REVERT: D  829 ARG cc_start: 0.8834 (mtp180) cc_final: 0.8423 (mtp180)
REVERT: D  898 MET cc_start: 0.8717 (tmm) cc_final: 0.8223 (tmm)
REVERT: D  903 TRP cc_start: 0.8739 (p-90) cc_final: 0.7869 (p-90)
REVERT: F   31 CYS cc_start: 0.2279 (OUTLIER) cc_final: 0.2009 (p)
REVERT: G   31 CYS cc_start: 0.1217 (OUTLIER) cc_final: 0.0869 (p)
  outliers start: 55
  outliers final: 32
  residues processed: 303
  average time/residue: 0.0823
  time to fit residues: 34.6235
Evaluate side-chains
  294 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 256
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
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  865 PHE
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  770 LEU
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  806 LEU
Chi-restraints excluded: chain B residue  810 GLU
Chi-restraints excluded: chain B residue  834 VAL
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  745 LEU
Chi-restraints excluded: chain C residue  797 SER
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  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  752 MET
Chi-restraints excluded: chain D residue  789 ILE
Chi-restraints excluded: chain D residue  797 SER
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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   chunk 12 optimal weight:    8.9990
   chunk 38 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 98 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 64 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0570
   chunk 87 optimal weight:    9.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    1.2900

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

Flipped N/Q/H residues before XYZ refinement:
A 728 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 = 0.146714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.113051 restraints weight = 20770.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.116540 restraints weight = 9113.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.118623 restraints weight = 5541.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.119538 restraints weight = 4222.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.120298 restraints weight = 3711.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.3652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8708  Z= 0.150
  Angle     :  0.725  12.985  11816  Z= 0.365
  Chirality :  0.042   0.357   1392
  Planarity :  0.004   0.035   1416
  Dihedral  :  5.810  51.511   1118
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 15.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 31.81 %
    Favored  : 62.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.26), residues: 1032
  helix:  0.40 (0.19), residues: 728
  sheet:  None (None), residues: 0
  loop : -1.01 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 841 
 TYR   0.019   0.002   TYR A 866 
 PHE   0.021   0.001   PHE D 802 
 TRP   0.014   0.001   TRP F  30 
 HIS   0.002   0.000   HIS D 787 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8708)
  covalent geometry    : angle       0.72532 (11816)
  hydrogen bonds       : bond        0.04587 (  573)
  hydrogen bonds       : angle       5.08653 ( 1599)

*********************** 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
  321 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 268
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  752 MET cc_start: 0.7439 (mpp) cc_final: 0.6315 (mmt)
REVERT: A  808 LEU cc_start: 0.8827 (mm) cc_final: 0.8535 (mm)
REVERT: A  829 ARG cc_start: 0.8786 (mtp180) cc_final: 0.8235 (mmm-85)
REVERT: A  903 TRP cc_start: 0.8788 (p-90) cc_final: 0.8031 (p-90)
REVERT: B  748 LEU cc_start: 0.9080 (mm) cc_final: 0.8856 (mm)
REVERT: B  829 ARG cc_start: 0.8791 (mtp180) cc_final: 0.7901 (mmm-85)
REVERT: B  874 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8277 (tm-30)
REVERT: B  903 TRP cc_start: 0.8788 (p-90) cc_final: 0.7906 (p-90)
REVERT: C  724 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7764 (tp)
REVERT: C  748 LEU cc_start: 0.9231 (mm) cc_final: 0.9013 (mm)
REVERT: C  750 MET cc_start: 0.8400 (tpt) cc_final: 0.8144 (tpt)
REVERT: C  840 MET cc_start: 0.6904 (mmm) cc_final: 0.6476 (mmp)
REVERT: D  749 PHE cc_start: 0.8440 (t80) cc_final: 0.8176 (t80)
REVERT: D  829 ARG cc_start: 0.8826 (mtp180) cc_final: 0.8084 (mmm-85)
REVERT: D  903 TRP cc_start: 0.8776 (p-90) cc_final: 0.7970 (p-90)
REVERT: G   31 CYS cc_start: 0.1148 (OUTLIER) cc_final: 0.0817 (p)
  outliers start: 53
  outliers final: 38
  residues processed: 296
  average time/residue: 0.0857
  time to fit residues: 35.3413
Evaluate side-chains
  295 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 255
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
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  865 PHE
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  770 LEU
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  806 LEU
Chi-restraints excluded: chain B residue  810 GLU
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  728 ASN
Chi-restraints excluded: chain C residue  745 LEU
Chi-restraints excluded: chain C residue  797 SER
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  728 ASN
Chi-restraints excluded: chain D residue  752 MET
Chi-restraints excluded: chain D residue  789 ILE
Chi-restraints excluded: chain D residue  797 SER
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    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 97 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 71 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   chunk 93 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9980
   chunk 26 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9980
   chunk 54 optimal weight:    9.9990
   overall best weight:    1.3384

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.146466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.113634 restraints weight = 20889.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.117119 restraints weight = 9144.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.119218 restraints weight = 5533.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.120361 restraints weight = 4167.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.120841 restraints weight = 3602.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.3887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8708  Z= 0.153
  Angle     :  0.750  13.336  11816  Z= 0.374
  Chirality :  0.043   0.386   1392
  Planarity :  0.004   0.034   1416
  Dihedral  :  5.755  52.191   1118
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 31.70 %
    Favored  : 62.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.26), residues: 1032
  helix:  0.39 (0.19), residues: 728
  sheet:  None (None), residues: 0
  loop : -1.05 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 841 
 TYR   0.010   0.002   TYR A 915 
 PHE   0.039   0.001   PHE A 802 
 TRP   0.017   0.001   TRP F  30 
 HIS   0.002   0.000   HIS C 787 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 8708)
  covalent geometry    : angle       0.75041 (11816)
  hydrogen bonds       : bond        0.04501 (  573)
  hydrogen bonds       : angle       5.05318 ( 1599)

*********************** 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
  320 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 267
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  752 MET cc_start: 0.7443 (mpp) cc_final: 0.6348 (mmt)
REVERT: A  808 LEU cc_start: 0.8800 (mm) cc_final: 0.8516 (mm)
REVERT: A  829 ARG cc_start: 0.8799 (mtp180) cc_final: 0.8248 (mmm-85)
REVERT: A  898 MET cc_start: 0.8736 (tmm) cc_final: 0.8203 (tmm)
REVERT: B  748 LEU cc_start: 0.9098 (mm) cc_final: 0.8824 (mm)
REVERT: B  752 MET cc_start: 0.8353 (ptp) cc_final: 0.7126 (mmt)
REVERT: B  829 ARG cc_start: 0.8812 (mtp180) cc_final: 0.7942 (mmm-85)
REVERT: B  903 TRP cc_start: 0.8816 (p-90) cc_final: 0.7946 (p-90)
REVERT: C  724 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7788 (tp)
REVERT: C  748 LEU cc_start: 0.9252 (mm) cc_final: 0.9026 (mm)
REVERT: C  750 MET cc_start: 0.8432 (tpt) cc_final: 0.8164 (tpt)
REVERT: C  808 LEU cc_start: 0.8766 (mm) cc_final: 0.8489 (mm)
REVERT: C  829 ARG cc_start: 0.8809 (mtp180) cc_final: 0.8048 (mmm-85)
REVERT: C  840 MET cc_start: 0.6995 (mmm) cc_final: 0.6555 (mmp)
REVERT: C  898 MET cc_start: 0.8716 (tmm) cc_final: 0.8211 (tmm)
REVERT: D  724 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7780 (tp)
REVERT: D  749 PHE cc_start: 0.8475 (t80) cc_final: 0.8101 (t80)
REVERT: D  829 ARG cc_start: 0.8819 (mtp180) cc_final: 0.8331 (mtp85)
REVERT: D  903 TRP cc_start: 0.8697 (p-90) cc_final: 0.7903 (p-90)
REVERT: G   31 CYS cc_start: 0.1093 (OUTLIER) cc_final: 0.0767 (p)
  outliers start: 53
  outliers final: 37
  residues processed: 295
  average time/residue: 0.0863
  time to fit residues: 35.1177
Evaluate side-chains
  296 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 256
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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  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  806 LEU
Chi-restraints excluded: chain B residue  810 GLU
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  728 ASN
Chi-restraints excluded: chain C residue  745 LEU
Chi-restraints excluded: chain C residue  789 ILE
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  936 LEU
Chi-restraints excluded: chain D residue  722 MET
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  728 ASN
Chi-restraints excluded: chain D residue  752 MET
Chi-restraints excluded: chain D residue  770 LEU
Chi-restraints excluded: chain D residue  789 ILE
Chi-restraints excluded: chain D residue  797 SER
Chi-restraints excluded: chain D residue  834 VAL
Chi-restraints excluded: chain D residue  936 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 56 optimal weight:    7.9990
   chunk 77 optimal weight:    9.9990
   chunk 5 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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
D 728 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.145776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.112701 restraints weight = 20855.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.116109 restraints weight = 9159.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.118196 restraints weight = 5549.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.119345 restraints weight = 4192.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.119820 restraints weight = 3629.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.4120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8708  Z= 0.161
  Angle     :  0.788  14.143  11816  Z= 0.391
  Chirality :  0.044   0.385   1392
  Planarity :  0.005   0.108   1416
  Dihedral  :  5.738  52.014   1118
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 33.40 %
    Favored  : 61.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.26), residues: 1032
  helix:  0.33 (0.19), residues: 728
  sheet:  None (None), residues: 0
  loop : -1.18 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 826 
 TYR   0.010   0.002   TYR A 915 
 PHE   0.031   0.001   PHE A 802 
 TRP   0.016   0.001   TRP F  30 
 HIS   0.002   0.000   HIS C 755 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 8708)
  covalent geometry    : angle       0.78820 (11816)
  hydrogen bonds       : bond        0.04467 (  573)
  hydrogen bonds       : angle       5.08749 ( 1599)

*********************** 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
  309 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 261
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  752 MET cc_start: 0.7566 (mpp) cc_final: 0.6475 (mmt)
REVERT: A  829 ARG cc_start: 0.8807 (mtp180) cc_final: 0.8259 (mmm-85)
REVERT: A  898 MET cc_start: 0.8811 (tmm) cc_final: 0.8277 (tmm)
REVERT: B  748 LEU cc_start: 0.9086 (mm) cc_final: 0.8714 (mm)
REVERT: B  752 MET cc_start: 0.8393 (ptp) cc_final: 0.7135 (tpt)
REVERT: B  829 ARG cc_start: 0.8802 (mtp180) cc_final: 0.8048 (mmm-85)
REVERT: B  903 TRP cc_start: 0.8864 (p-90) cc_final: 0.8081 (p-90)
REVERT: C  724 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7782 (tp)
REVERT: C  748 LEU cc_start: 0.9297 (mm) cc_final: 0.9001 (mm)
REVERT: C  750 MET cc_start: 0.8465 (tpt) cc_final: 0.8218 (tpt)
REVERT: C  829 ARG cc_start: 0.8824 (mtp180) cc_final: 0.8068 (mmm-85)
REVERT: C  840 MET cc_start: 0.6921 (mmm) cc_final: 0.6489 (mmp)
REVERT: C  898 MET cc_start: 0.8758 (tmm) cc_final: 0.8226 (tmm)
REVERT: D  724 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7713 (mt)
REVERT: D  749 PHE cc_start: 0.8502 (t80) cc_final: 0.8145 (t80)
REVERT: D  808 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7894 (mm)
REVERT: D  829 ARG cc_start: 0.8791 (mtp180) cc_final: 0.8480 (mtp85)
REVERT: D  903 TRP cc_start: 0.8742 (p-90) cc_final: 0.7929 (p-90)
REVERT: G   31 CYS cc_start: 0.1170 (OUTLIER) cc_final: 0.0805 (p)
  outliers start: 48
  outliers final: 34
  residues processed: 286
  average time/residue: 0.0843
  time to fit residues: 33.3927
Evaluate side-chains
  295 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 257
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
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  931 PHE
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  806 LEU
Chi-restraints excluded: chain B residue  810 GLU
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  745 LEU
Chi-restraints excluded: chain C residue  789 ILE
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  936 LEU
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  728 ASN
Chi-restraints excluded: chain D residue  770 LEU
Chi-restraints excluded: chain D residue  797 SER
Chi-restraints excluded: chain D residue  808 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    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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   chunk 6 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 66 optimal weight:   20.0000
   chunk 25 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 93 optimal weight:    5.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
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 = 0.4187 r_free = 0.4187 target = 0.147046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.114846 restraints weight = 20478.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.118123 restraints weight = 9183.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.120100 restraints weight = 5642.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.121201 restraints weight = 4287.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.121671 restraints weight = 3722.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.4224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8708  Z= 0.160
  Angle     :  0.795  13.886  11816  Z= 0.393
  Chirality :  0.044   0.402   1392
  Planarity :  0.004   0.038   1416
  Dihedral  :  5.738  52.054   1118
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 17.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 34.47 %
    Favored  : 61.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.26), residues: 1032
  helix:  0.38 (0.19), residues: 728
  sheet:  None (None), residues: 0
  loop : -1.17 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 826 
 TYR   0.018   0.002   TYR D 866 
 PHE   0.033   0.001   PHE A 802 
 TRP   0.018   0.001   TRP F  30 
 HIS   0.001   0.000   HIS C 787 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 8708)
  covalent geometry    : angle       0.79472 (11816)
  hydrogen bonds       : bond        0.04424 (  573)
  hydrogen bonds       : angle       5.06100 ( 1599)

********************** 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
  305 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 263
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  752 MET cc_start: 0.7581 (mpp) cc_final: 0.6490 (mmt)
REVERT: A  898 MET cc_start: 0.8745 (tmm) cc_final: 0.8225 (tmm)
REVERT: B  748 LEU cc_start: 0.8991 (mm) cc_final: 0.8702 (mm)
REVERT: B  752 MET cc_start: 0.8339 (ptp) cc_final: 0.6861 (tpp)
REVERT: B  808 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8082 (mm)
REVERT: B  829 ARG cc_start: 0.8814 (mtp180) cc_final: 0.8050 (mmm-85)
REVERT: B  903 TRP cc_start: 0.8929 (p-90) cc_final: 0.8092 (p-90)
REVERT: C  724 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7775 (tp)
REVERT: C  748 LEU cc_start: 0.9235 (mm) cc_final: 0.9012 (mm)
REVERT: C  750 MET cc_start: 0.8518 (tpt) cc_final: 0.8309 (tpt)
REVERT: C  808 LEU cc_start: 0.8729 (mm) cc_final: 0.8454 (mm)
REVERT: C  829 ARG cc_start: 0.8835 (mtp180) cc_final: 0.8071 (mmm-85)
REVERT: C  840 MET cc_start: 0.6872 (mmm) cc_final: 0.6464 (mmp)
REVERT: C  898 MET cc_start: 0.8705 (tmm) cc_final: 0.8207 (tmm)
REVERT: D  749 PHE cc_start: 0.8496 (t80) cc_final: 0.8091 (t80)
REVERT: D  759 GLU cc_start: 0.8433 (tp30) cc_final: 0.7486 (pm20)
REVERT: D  800 ASP cc_start: 0.8146 (m-30) cc_final: 0.7453 (t70)
REVERT: D  826 ARG cc_start: 0.8193 (ttp-110) cc_final: 0.7882 (mmm-85)
REVERT: D  831 PHE cc_start: 0.6615 (t80) cc_final: 0.6389 (t80)
REVERT: D  903 TRP cc_start: 0.8830 (p-90) cc_final: 0.7953 (p-90)
REVERT: F    6 PHE cc_start: 0.6393 (m-10) cc_final: 0.6101 (m-10)
REVERT: G   31 CYS cc_start: 0.1193 (OUTLIER) cc_final: 0.0829 (p)
  outliers start: 42
  outliers final: 31
  residues processed: 282
  average time/residue: 0.0848
  time to fit residues: 33.2484
Evaluate side-chains
  296 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 262
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  931 PHE
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  808 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  745 LEU
Chi-restraints excluded: chain C residue  789 ILE
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  936 LEU
Chi-restraints excluded: chain D residue  728 ASN
Chi-restraints excluded: chain D residue  770 LEU
Chi-restraints excluded: chain D residue  789 ILE
Chi-restraints excluded: chain D residue  797 SER
Chi-restraints excluded: chain D residue  834 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    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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 26 optimal weight:   20.0000
   chunk 9 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   chunk 78 optimal weight:    7.9990
   chunk 96 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 44 optimal weight:   20.0000
   chunk 43 optimal weight:   10.0000
   chunk 84 optimal weight:    2.9990
   chunk 66 optimal weight:   20.0000
   chunk 46 optimal weight:    5.9990
   overall best weight:    5.3990

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.141582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.107213 restraints weight = 21060.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.110423 restraints weight = 9463.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.112278 restraints weight = 5924.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.113291 restraints weight = 4597.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.113800 restraints weight = 4042.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.4257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   8708  Z= 0.259
  Angle     :  0.856  14.726  11816  Z= 0.429
  Chirality :  0.047   0.347   1392
  Planarity :  0.005   0.034   1416
  Dihedral  :  5.794  52.724   1116
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 19.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 34.26 %
    Favored  : 61.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.25), residues: 1032
  helix:  0.13 (0.19), residues: 728
  sheet:  None (None), residues: 0
  loop : -1.27 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 826 
 TYR   0.019   0.003   TYR D 915 
 PHE   0.024   0.002   PHE B 831 
 TRP   0.019   0.002   TRP F  30 
 HIS   0.001   0.001   HIS B 755 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 ( 8708)
  covalent geometry    : angle       0.85649 (11816)
  hydrogen bonds       : bond        0.04592 (  573)
  hydrogen bonds       : angle       5.36218 ( 1599)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1733.09 seconds
wall clock time: 30 minutes 27.79 seconds (1827.79 seconds total)