Starting phenix.real_space_refine
on Sat May 10 05:53:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g5i_51087/05_2025/9g5i_51087_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g5i_51087/05_2025/9g5i_51087.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g5i_51087/05_2025/9g5i_51087.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g5i_51087/05_2025/9g5i_51087.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g5i_51087/05_2025/9g5i_51087_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g5i_51087/05_2025/9g5i_51087_neut.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      45      5.16       5
     C    3253      2.51       5
     N     938      2.21       5
     O    1016      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5252
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2363
          Classifications: {'peptide': 331}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 316}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 25
    Chain: "B"
      Number of atoms: 2436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 345, 2436
          Classifications: {'peptide': 345}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 2, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 37
    Chain: "C"
      Number of atoms: 453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 453
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
  Time building chain proxies: 3.52, per 1000 atoms: 0.67
  Number of scatterers: 5252
  At special positions: 0
  Unit cell: (79.296, 85.904, 93.338, 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      45     16.00
     O    1016      8.00
     N     938      7.00
     C    3253      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 688 " - pdb=" SG  CYS A 701 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 783 " - pdb=" SG  CYS A 794 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 906 " - pdb=" SG  CYS A 928 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 987 " - pdb=" SG  CYS A 995 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 990 " - pdb=" SG  CYS A1006 " distance=2.06
    Simple disulfide: pdb=" SG  CYS B 688 " - pdb=" SG  CYS B 701 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 783 " - pdb=" SG  CYS B 794 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 906 " - pdb=" SG  CYS B 928 " distance=2.07
    Simple disulfide: pdb=" SG  CYS B 987 " - pdb=" SG  CYS B 995 " distance=2.06
    Simple disulfide: pdb=" SG  CYS B 990 " - pdb=" SG  CYS B1006 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B1008 " - pdb=" SG  CYS B1021 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 111 " - pdb=" SG  CYS C 147 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C 125 " - pdb=" SG  CYS C 134 " distance=2.01

  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: 1.17
  Conformation dependent library (CDL) restraints added in 643.0 milliseconds
  

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1198

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 6 sheets defined
      19.1% alpha, 19.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 697 through 705
    Processing helix  chain 'A' and resid 717 through 721
      removed outlier: 3.668A  pdb=" N   LEU A 720 " --> pdb=" O   GLU A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 796
    Processing helix  chain 'A' and resid 799 through 808
      removed outlier: 3.586A  pdb=" N   ARG A 806 " --> pdb=" O   GLU A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 899
    Processing helix  chain 'A' and resid 906 through 911
    Processing helix  chain 'A' and resid 986 through 990
      removed outlier: 3.749A  pdb=" N   CYS A 990 " --> pdb=" O   CYS A 987 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 697 through 705
    Processing helix  chain 'B' and resid 717 through 721
      removed outlier: 4.224A  pdb=" N   LEU B 720 " --> pdb=" O   GLU B 717 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 787 through 795
    Processing helix  chain 'B' and resid 799 through 809
    Processing helix  chain 'B' and resid 895 through 899
    Processing helix  chain 'B' and resid 906 through 911
    Processing helix  chain 'C' and resid 95 through 103
    Processing helix  chain 'C' and resid 108 through 122
      removed outlier: 3.789A  pdb=" N   THR C 122 " --> pdb=" O   LEU C 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 127
      removed outlier: 3.575A  pdb=" N   ILE C 127 " --> pdb=" O   ARG C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 144
    Processing sheet with id=AA1, first strand: chain 'A' and resid 682 through 685
    Processing sheet with id=AA2, first strand: chain 'A' and resid 682 through 685
      removed outlier: 5.386A  pdb=" N   GLY A 756 " --> pdb=" O   VAL A 972 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 713 through 714
      removed outlier: 3.501A  pdb=" N   GLU A 713 " --> pdb=" O   ILE A 725 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   MET A 770 " --> pdb=" O   MET A 830 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   MET A 830 " --> pdb=" O   MET A 770 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   THR A 825 " --> pdb=" O   ILE A 840 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   ILE A 840 " --> pdb=" O   THR A 825 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL A 827 " --> pdb=" O   LEU A 838 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   GLU A 862 " --> pdb=" O   ILE A 959 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 682 through 685
      removed outlier: 5.347A  pdb=" N   GLY B 756 " --> pdb=" O   VAL B 972 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU B 970 " --> pdb=" O   SER B 758 " (cutoff:3.500A)
      removed outlier: 5.455A  pdb=" N   LEU B 760 " --> pdb=" O   PRO B 968 " (cutoff:3.500A)
      removed outlier: 8.203A  pdb=" N   ILE B 762 " --> pdb=" O   TYR B 966 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   TYR B 966 " --> pdb=" O   ILE B 762 " (cutoff:3.500A)
      removed outlier: 8.576A  pdb=" N   ASN B 764 " --> pdb=" O   ILE B 964 " (cutoff:3.500A)
      removed outlier: 9.301A  pdb=" N   ILE B 964 " --> pdb=" O   ASN B 764 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 713 through 714
      removed outlier: 6.600A  pdb=" N   MET B 770 " --> pdb=" O   MET B 830 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   MET B 830 " --> pdb=" O   MET B 770 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LYS B 829 " --> pdb=" O   PRO B 837 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   LYS B 831 " --> pdb=" O   PRO B 835 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ARG B 860 " --> pdb=" O   SER B 957 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   ILE B 959 " --> pdb=" O   ARG B 860 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   GLU B 862 " --> pdb=" O   ILE B 959 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 995 through 997

    166 hydrogen bonds defined for protein.
    438 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: 1.30

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 964
        1.32 -     1.44: 1445
        1.44 -     1.57: 2900
        1.57 -     1.70: 0
        1.70 -     1.83: 63
  Bond restraints: 5372
  Sorted by residual:
  bond pdb=" C   GLY B 924 "
       pdb=" O   GLY B 924 "
    ideal  model  delta    sigma   weight residual
    1.243  1.204  0.038 9.30e-03 1.16e+04 1.69e+01
  bond pdb=" C   GLY B 844 "
       pdb=" O   GLY B 844 "
    ideal  model  delta    sigma   weight residual
    1.237  1.207  0.030 9.70e-03 1.06e+04 9.87e+00
  bond pdb=" N   ASP B1009 "
       pdb=" CA  ASP B1009 "
    ideal  model  delta    sigma   weight residual
    1.454  1.491 -0.037 1.17e-02 7.31e+03 9.83e+00
  bond pdb=" N   VAL B1013 "
       pdb=" CA  VAL B1013 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.036 1.17e-02 7.31e+03 9.62e+00
  bond pdb=" CA  SER A 754 "
       pdb=" CB  SER A 754 "
    ideal  model  delta    sigma   weight residual
    1.529  1.480  0.049 1.64e-02 3.72e+03 8.84e+00
  ... (remaining 5367 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 6674
        1.73 -     3.47: 535
        3.47 -     5.20: 55
        5.20 -     6.94: 5
        6.94 -     8.67: 1
  Bond angle restraints: 7270
  Sorted by residual:
  angle pdb=" NE  ARG C 136 "
        pdb=" CZ  ARG C 136 "
        pdb=" NH2 ARG C 136 "
      ideal   model   delta    sigma   weight residual
     119.20  122.73   -3.53 9.00e-01 1.23e+00 1.54e+01
  angle pdb=" N   PRO B 999 "
        pdb=" CA  PRO B 999 "
        pdb=" C   PRO B 999 "
      ideal   model   delta    sigma   weight residual
     113.53  108.20    5.33 1.39e+00 5.18e-01 1.47e+01
  angle pdb=" CA  ASP B 832 "
        pdb=" CB  ASP B 832 "
        pdb=" CG  ASP B 832 "
      ideal   model   delta    sigma   weight residual
     112.60  116.43   -3.83 1.00e+00 1.00e+00 1.46e+01
  angle pdb=" N   TRP A 913 "
        pdb=" CA  TRP A 913 "
        pdb=" C   TRP A 913 "
      ideal   model   delta    sigma   weight residual
     114.75  110.17    4.58 1.26e+00 6.30e-01 1.32e+01
  angle pdb=" C   ASP B 832 "
        pdb=" N   GLY B 833 "
        pdb=" CA  GLY B 833 "
      ideal   model   delta    sigma   weight residual
     123.30  119.52    3.78 1.06e+00 8.90e-01 1.27e+01
  ... (remaining 7265 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.13: 2848
       18.13 -    36.25: 201
       36.25 -    54.37: 36
       54.37 -    72.50: 15
       72.50 -    90.62: 6
  Dihedral angle restraints: 3106
    sinusoidal: 1157
      harmonic: 1949
  Sorted by residual:
  dihedral pdb=" CA  ILE A 805 "
           pdb=" C   ILE A 805 "
           pdb=" N   ARG A 806 "
           pdb=" CA  ARG A 806 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.65   26.35     0      5.00e+00 4.00e-02 2.78e+01
  dihedral pdb=" CA  MET A 830 "
           pdb=" C   MET A 830 "
           pdb=" N   LYS A 831 "
           pdb=" CA  LYS A 831 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.55   25.45     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CB  CYS B 906 "
           pdb=" SG  CYS B 906 "
           pdb=" SG  CYS B 928 "
           pdb=" CB  CYS B 928 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -44.55  -41.45     1      1.00e+01 1.00e-02 2.40e+01
  ... (remaining 3103 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 381
       0.051 -    0.103: 255
       0.103 -    0.154: 86
       0.154 -    0.206: 21
       0.206 -    0.257: 10
  Chirality restraints: 753
  Sorted by residual:
  chirality pdb=" CA  PRO C 109 "
            pdb=" N   PRO C 109 "
            pdb=" C   PRO C 109 "
            pdb=" CB  PRO C 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  ASP B 832 "
            pdb=" N   ASP B 832 "
            pdb=" C   ASP B 832 "
            pdb=" CB  ASP B 832 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.25 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  VAL B 728 "
            pdb=" N   VAL B 728 "
            pdb=" C   VAL B 728 "
            pdb=" CB  VAL B 728 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 750 not shown)

  Planarity restraints: 975
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 883 "   -0.032 2.00e-02 2.50e+03   3.51e-02 3.08e+01
        pdb=" CG  TRP A 883 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 883 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 883 "    0.027 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 883 "    0.025 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 883 "    0.027 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 883 "    0.032 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 883 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 883 "    0.033 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 883 "   -0.082 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 739 "    0.045 2.00e-02 2.50e+03   3.52e-02 2.48e+01
        pdb=" CG  TYR B 739 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 739 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 739 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 739 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 739 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 739 "    0.068 2.00e-02 2.50e+03
        pdb=" OH  TYR B 739 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 123 "    0.321 9.50e-02 1.11e+02   1.45e-01 1.75e+01
        pdb=" NE  ARG C 123 "   -0.032 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 123 "    0.034 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 123 "   -0.015 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 123 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 972 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1274
        2.79 -     3.32: 4915
        3.32 -     3.84: 8979
        3.84 -     4.37: 11019
        4.37 -     4.90: 18136
  Nonbonded interactions: 44323
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 895 "
            pdb=" OE1 GLU B 898 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   VAL B 867 "
            pdb=" OH  TYR B 937 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   VAL B 972 "
            pdb=" NH1 ARG C 136 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" NH2 ARG B 753 "
            pdb=" OD1 ASP B 781 "
     model   vdw
     2.317 3.120
  nonbonded pdb=" O   PRO C 109 "
            pdb=" OG  SER C 112 "
     model   vdw
     2.330 3.040
  ... (remaining 44318 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 678 through 985 or (resid 986 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 987 through 1008))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.930
  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:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     15.340
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
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   0.070   5385  Z= 0.617
  Angle     :  1.027   8.672   7296  Z= 0.666
  Chirality :  0.075   0.257    753
  Planarity :  0.009   0.145    975
  Dihedral  : 13.936  90.619   1869
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.27), residues: 726
  helix: -1.17 (0.45), residues: 106
  sheet: -1.29 (0.30), residues: 201
  loop : -1.22 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.082   0.010   TRP A 883 
 HIS   0.016   0.004   HIS A 983 
 PHE   0.028   0.007   PHE C 107 
 TYR   0.068   0.009   TYR B 739 
 ARG   0.038   0.003   ARG C 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18941 (  148)
  hydrogen bonds       : angle       7.36429 (  438)
  SS BOND              : bond        0.02224 (   13)
  SS BOND              : angle       1.65582 (   26)
  covalent geometry    : bond        0.00978 ( 5372)
  covalent geometry    : angle       1.02419 ( 7270)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  997 MET cc_start: 0.5168 (ttp) cc_final: 0.4519 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1557
  time to fit residues: 23.5650
Evaluate side-chains
  99 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0020
   chunk 21 optimal weight:    0.3980
   chunk 34 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.6392

-------------------------------------------------------------------------------
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 = 0.3879 r_free = 0.3879 target = 0.139368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.116181 restraints weight = 8944.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 3.62
r_work: 0.3448 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.1100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5385  Z= 0.130
  Angle     :  0.558   8.274   7296  Z= 0.295
  Chirality :  0.046   0.161    753
  Planarity :  0.004   0.053    975
  Dihedral  :  4.734  27.914    768
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  6.65 %
    Favored  : 92.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.29), residues: 726
  helix:  0.01 (0.49), residues: 110
  sheet: -0.94 (0.31), residues: 191
  loop : -1.09 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 814 
 HIS   0.002   0.001   HIS A 904 
 PHE   0.025   0.002   PHE A 685 
 TYR   0.014   0.001   TYR C 130 
 ARG   0.005   0.001   ARG C 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04570 (  148)
  hydrogen bonds       : angle       5.65187 (  438)
  SS BOND              : bond        0.00316 (   13)
  SS BOND              : angle       0.84353 (   26)
  covalent geometry    : bond        0.00277 ( 5372)
  covalent geometry    : angle       0.55703 ( 7270)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 115
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  770 MET cc_start: 0.6892 (mmm) cc_final: 0.6683 (mmt)
REVERT: A  997 MET cc_start: 0.3497 (ttp) cc_final: 0.2786 (mtp)
REVERT: B  947 ASP cc_start: 0.8246 (t0) cc_final: 0.8028 (t70)
REVERT: C  113 LYS cc_start: 0.7748 (tppt) cc_final: 0.7510 (tppp)
REVERT: C  130 TYR cc_start: 0.7937 (m-10) cc_final: 0.7503 (m-80)
REVERT: C  132 LYS cc_start: 0.8338 (mmmm) cc_final: 0.8131 (mmtm)
  outliers start: 2
  outliers final: 1
  residues processed: 115
  average time/residue: 0.1601
  time to fit residues: 24.2536
Evaluate side-chains
  99 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  985 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 59 optimal weight:    8.9990
   chunk 50 optimal weight:    5.9990
   chunk 6 optimal weight:    8.9990
   chunk 54 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 32 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
B 983 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.136733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.112519 restraints weight = 8835.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 3.60
r_work: 0.3424 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   5385  Z= 0.309
  Angle     :  0.666   9.100   7296  Z= 0.357
  Chirality :  0.050   0.172    753
  Planarity :  0.005   0.064    975
  Dihedral  :  5.113  26.548    768
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 11.22 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.29), residues: 726
  helix:  0.18 (0.51), residues: 109
  sheet: -1.13 (0.32), residues: 187
  loop : -1.25 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 814 
 HIS   0.005   0.001   HIS A 812 
 PHE   0.020   0.003   PHE A 828 
 TYR   0.016   0.002   TYR B 739 
 ARG   0.007   0.001   ARG C 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05122 (  148)
  hydrogen bonds       : angle       5.78474 (  438)
  SS BOND              : bond        0.00549 (   13)
  SS BOND              : angle       1.41333 (   26)
  covalent geometry    : bond        0.00660 ( 5372)
  covalent geometry    : angle       0.66192 ( 7270)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  997 MET cc_start: 0.6801 (tpt) cc_final: 0.3763 (ptm)
REVERT: C  130 TYR cc_start: 0.8241 (m-10) cc_final: 0.7970 (m-80)
REVERT: C  132 LYS cc_start: 0.8536 (mmmm) cc_final: 0.8313 (mmtm)
  outliers start: 10
  outliers final: 8
  residues processed: 108
  average time/residue: 0.1484
  time to fit residues: 21.3955
Evaluate side-chains
  105 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  831 LYS
Chi-restraints excluded: chain A residue  886 ASN
Chi-restraints excluded: chain A residue  951 ASP
Chi-restraints excluded: chain B residue  714 VAL
Chi-restraints excluded: chain B residue  764 ASN
Chi-restraints excluded: chain B residue  781 ASP
Chi-restraints excluded: chain B residue  801 ILE
Chi-restraints excluded: chain B residue  972 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 32 optimal weight:    0.1980
   chunk 22 optimal weight:    0.9980
   chunk 61 optimal weight:    0.1980
   chunk 70 optimal weight:    0.0980
   chunk 34 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0050
   chunk 18 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.2794

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

Flipped N/Q/H residues before XYZ refinement:
A 989 HIS
B 707 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.144106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.119891 restraints weight = 8800.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 3.67
r_work: 0.3538 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5385  Z= 0.108
  Angle     :  0.550   9.934   7296  Z= 0.284
  Chirality :  0.045   0.169    753
  Planarity :  0.004   0.061    975
  Dihedral  :  4.559  26.712    768
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.50 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.29), residues: 726
  helix:  0.49 (0.52), residues: 109
  sheet: -0.65 (0.35), residues: 172
  loop : -1.16 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 883 
 HIS   0.003   0.001   HIS A 904 
 PHE   0.011   0.001   PHE A 685 
 TYR   0.009   0.001   TYR A 826 
 ARG   0.004   0.000   ARG C 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03708 (  148)
  hydrogen bonds       : angle       5.26079 (  438)
  SS BOND              : bond        0.00299 (   13)
  SS BOND              : angle       0.94895 (   26)
  covalent geometry    : bond        0.00226 ( 5372)
  covalent geometry    : angle       0.54799 ( 7270)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.593 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  753 ARG cc_start: 0.7111 (ptp-110) cc_final: 0.6886 (ptp-110)
REVERT: A  770 MET cc_start: 0.6840 (mmm) cc_final: 0.6605 (mmp)
REVERT: B  997 MET cc_start: 0.6546 (tpt) cc_final: 0.3619 (ptm)
REVERT: C  113 LYS cc_start: 0.7863 (tppp) cc_final: 0.7588 (tppp)
REVERT: C  130 TYR cc_start: 0.8062 (m-10) cc_final: 0.7751 (m-80)
  outliers start: 11
  outliers final: 7
  residues processed: 111
  average time/residue: 0.1618
  time to fit residues: 23.9099
Evaluate side-chains
  109 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  836 VAL
Chi-restraints excluded: chain A residue  930 SER
Chi-restraints excluded: chain A residue  951 ASP
Chi-restraints excluded: chain A residue 1006 CYS
Chi-restraints excluded: chain B residue  764 ASN
Chi-restraints excluded: chain B residue  781 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0980
   chunk 1 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 52 optimal weight:    8.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 = 0.3914 r_free = 0.3914 target = 0.139615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.115742 restraints weight = 8710.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 3.59
r_work: 0.3476 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5385  Z= 0.189
  Angle     :  0.570   6.419   7296  Z= 0.301
  Chirality :  0.046   0.161    753
  Planarity :  0.004   0.061    975
  Dihedral  :  4.657  26.868    768
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 13.50 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.30), residues: 726
  helix:  0.44 (0.52), residues: 109
  sheet: -0.98 (0.33), residues: 186
  loop : -1.08 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 814 
 HIS   0.004   0.001   HIS A 989 
 PHE   0.020   0.002   PHE A 828 
 TYR   0.012   0.001   TYR A 937 
 ARG   0.003   0.001   ARG B 918 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04128 (  148)
  hydrogen bonds       : angle       5.30374 (  438)
  SS BOND              : bond        0.00354 (   13)
  SS BOND              : angle       1.04315 (   26)
  covalent geometry    : bond        0.00400 ( 5372)
  covalent geometry    : angle       0.56795 ( 7270)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  868 LEU cc_start: 0.8413 (tt) cc_final: 0.8114 (mp)
REVERT: B  734 TYR cc_start: 0.8298 (m-80) cc_final: 0.8092 (m-80)
REVERT: B  908 GLN cc_start: 0.8202 (tp40) cc_final: 0.7990 (tp40)
REVERT: B  997 MET cc_start: 0.6682 (tpt) cc_final: 0.3667 (ptm)
REVERT: C  113 LYS cc_start: 0.7945 (tppp) cc_final: 0.7608 (tppp)
REVERT: C  130 TYR cc_start: 0.8194 (m-10) cc_final: 0.7844 (m-80)
  outliers start: 14
  outliers final: 11
  residues processed: 109
  average time/residue: 0.1604
  time to fit residues: 23.2444
Evaluate side-chains
  111 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  831 LYS
Chi-restraints excluded: chain A residue  836 VAL
Chi-restraints excluded: chain A residue  886 ASN
Chi-restraints excluded: chain A residue  930 SER
Chi-restraints excluded: chain A residue  951 ASP
Chi-restraints excluded: chain A residue 1006 CYS
Chi-restraints excluded: chain B residue  714 VAL
Chi-restraints excluded: chain B residue  764 ASN
Chi-restraints excluded: chain B residue  781 ASP
Chi-restraints excluded: chain B residue  906 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0000
   chunk 47 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.7188

-------------------------------------------------------------------------------
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 = 0.3953 r_free = 0.3953 target = 0.142518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.118744 restraints weight = 8703.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 3.59
r_work: 0.3518 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5385  Z= 0.124
  Angle     :  0.535   6.890   7296  Z= 0.280
  Chirality :  0.045   0.162    753
  Planarity :  0.004   0.061    975
  Dihedral  :  4.476  27.029    768
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.97 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.30), residues: 726
  helix:  0.41 (0.51), residues: 109
  sheet: -0.89 (0.33), residues: 187
  loop : -1.05 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 814 
 HIS   0.002   0.001   HIS A 904 
 PHE   0.009   0.001   PHE A 828 
 TYR   0.009   0.001   TYR B 739 
 ARG   0.002   0.000   ARG A 847 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03669 (  148)
  hydrogen bonds       : angle       5.15486 (  438)
  SS BOND              : bond        0.00270 (   13)
  SS BOND              : angle       0.88571 (   26)
  covalent geometry    : bond        0.00264 ( 5372)
  covalent geometry    : angle       0.53366 ( 7270)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  753 ARG cc_start: 0.7063 (ptp-110) cc_final: 0.6853 (ptp-110)
REVERT: A  831 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7749 (ptpt)
REVERT: A  868 LEU cc_start: 0.8322 (tt) cc_final: 0.8062 (mp)
REVERT: B  734 TYR cc_start: 0.8246 (m-80) cc_final: 0.8016 (m-80)
REVERT: B  908 GLN cc_start: 0.8223 (tp40) cc_final: 0.7974 (tp40)
REVERT: B  974 GLU cc_start: 0.7466 (pt0) cc_final: 0.7260 (pt0)
REVERT: B  997 MET cc_start: 0.6560 (tpt) cc_final: 0.3663 (ptm)
REVERT: C  113 LYS cc_start: 0.7921 (tppp) cc_final: 0.7676 (tppp)
REVERT: C  130 TYR cc_start: 0.8118 (m-10) cc_final: 0.7795 (m-80)
  outliers start: 13
  outliers final: 10
  residues processed: 116
  average time/residue: 0.1599
  time to fit residues: 24.4944
Evaluate side-chains
  112 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  831 LYS
Chi-restraints excluded: chain A residue  836 VAL
Chi-restraints excluded: chain A residue  886 ASN
Chi-restraints excluded: chain A residue  930 SER
Chi-restraints excluded: chain A residue  951 ASP
Chi-restraints excluded: chain A residue 1006 CYS
Chi-restraints excluded: chain B residue  764 ASN
Chi-restraints excluded: chain B residue  781 ASP
Chi-restraints excluded: chain B residue  906 CYS
Chi-restraints excluded: chain B residue  972 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 65 optimal weight:    0.4980
   chunk 4 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 777 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.142118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.118308 restraints weight = 8611.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 3.59
r_work: 0.3513 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5385  Z= 0.135
  Angle     :  0.543   7.067   7296  Z= 0.284
  Chirality :  0.046   0.171    753
  Planarity :  0.004   0.060    975
  Dihedral  :  4.465  27.111    768
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.59 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.30), residues: 726
  helix:  0.44 (0.51), residues: 109
  sheet: -0.81 (0.33), residues: 189
  loop : -1.03 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 814 
 HIS   0.002   0.001   HIS A 904 
 PHE   0.017   0.001   PHE A 828 
 TYR   0.009   0.001   TYR B 739 
 ARG   0.003   0.000   ARG A 847 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03662 (  148)
  hydrogen bonds       : angle       5.10600 (  438)
  SS BOND              : bond        0.00266 (   13)
  SS BOND              : angle       0.84394 (   26)
  covalent geometry    : bond        0.00291 ( 5372)
  covalent geometry    : angle       0.54140 ( 7270)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  753 ARG cc_start: 0.7053 (ptp-110) cc_final: 0.6802 (ptp-110)
REVERT: A  831 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7699 (ptpt)
REVERT: A  868 LEU cc_start: 0.8330 (tt) cc_final: 0.8069 (mp)
REVERT: B  734 TYR cc_start: 0.8268 (m-80) cc_final: 0.8015 (m-80)
REVERT: B  908 GLN cc_start: 0.8238 (tp40) cc_final: 0.7972 (tp40)
REVERT: B  997 MET cc_start: 0.6596 (tpt) cc_final: 0.3686 (ptm)
REVERT: C  113 LYS cc_start: 0.7875 (tppp) cc_final: 0.7620 (tppp)
REVERT: C  130 TYR cc_start: 0.8095 (m-10) cc_final: 0.7768 (m-80)
  outliers start: 14
  outliers final: 13
  residues processed: 109
  average time/residue: 0.1513
  time to fit residues: 21.8934
Evaluate side-chains
  114 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  831 LYS
Chi-restraints excluded: chain A residue  836 VAL
Chi-restraints excluded: chain A residue  886 ASN
Chi-restraints excluded: chain A residue  930 SER
Chi-restraints excluded: chain A residue  951 ASP
Chi-restraints excluded: chain A residue 1006 CYS
Chi-restraints excluded: chain B residue  764 ASN
Chi-restraints excluded: chain B residue  781 ASP
Chi-restraints excluded: chain B residue  864 ASN
Chi-restraints excluded: chain B residue  906 CYS
Chi-restraints excluded: chain B residue  972 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0870
   chunk 49 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.7362

-------------------------------------------------------------------------------
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 = 0.3956 r_free = 0.3956 target = 0.142860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.119067 restraints weight = 8566.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 3.59
r_work: 0.3527 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5385  Z= 0.126
  Angle     :  0.539   7.591   7296  Z= 0.281
  Chirality :  0.045   0.158    753
  Planarity :  0.004   0.059    975
  Dihedral  :  4.406  27.323    768
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.59 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.30), residues: 726
  helix:  0.41 (0.51), residues: 109
  sheet: -0.82 (0.33), residues: 191
  loop : -1.04 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 814 
 HIS   0.002   0.001   HIS A 904 
 PHE   0.011   0.001   PHE A 828 
 TYR   0.009   0.001   TYR B 739 
 ARG   0.003   0.000   ARG A 847 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03561 (  148)
  hydrogen bonds       : angle       5.02163 (  438)
  SS BOND              : bond        0.00244 (   13)
  SS BOND              : angle       0.75637 (   26)
  covalent geometry    : bond        0.00270 ( 5372)
  covalent geometry    : angle       0.53808 ( 7270)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  753 ARG cc_start: 0.7016 (ptp-110) cc_final: 0.6760 (ptp-110)
REVERT: A  770 MET cc_start: 0.6541 (mmp) cc_final: 0.6179 (mmm)
REVERT: A  831 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7707 (ptpt)
REVERT: A  868 LEU cc_start: 0.8321 (tt) cc_final: 0.8078 (mp)
REVERT: B  734 TYR cc_start: 0.8259 (m-80) cc_final: 0.8021 (m-80)
REVERT: B  908 GLN cc_start: 0.8246 (tp40) cc_final: 0.7970 (tp40)
REVERT: B  997 MET cc_start: 0.6530 (tpt) cc_final: 0.3623 (ptm)
REVERT: C  113 LYS cc_start: 0.7900 (tppp) cc_final: 0.7652 (tppp)
REVERT: C  130 TYR cc_start: 0.8099 (m-10) cc_final: 0.7767 (m-80)
  outliers start: 15
  outliers final: 14
  residues processed: 110
  average time/residue: 0.1600
  time to fit residues: 23.1065
Evaluate side-chains
  118 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  831 LYS
Chi-restraints excluded: chain A residue  836 VAL
Chi-restraints excluded: chain A residue  886 ASN
Chi-restraints excluded: chain A residue  930 SER
Chi-restraints excluded: chain A residue  951 ASP
Chi-restraints excluded: chain A residue 1006 CYS
Chi-restraints excluded: chain B residue  714 VAL
Chi-restraints excluded: chain B residue  764 ASN
Chi-restraints excluded: chain B residue  781 ASP
Chi-restraints excluded: chain B residue  864 ASN
Chi-restraints excluded: chain B residue  906 CYS
Chi-restraints excluded: chain B residue  972 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   chunk 31 optimal weight:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 62 optimal weight:    0.2980
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.9986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.141905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.117969 restraints weight = 8652.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 3.60
r_work: 0.3512 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5385  Z= 0.147
  Angle     :  0.551   7.688   7296  Z= 0.289
  Chirality :  0.046   0.159    753
  Planarity :  0.004   0.059    975
  Dihedral  :  4.459  27.420    768
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.40 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.30), residues: 726
  helix:  0.34 (0.51), residues: 109
  sheet: -0.70 (0.33), residues: 184
  loop : -1.04 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 814 
 HIS   0.002   0.001   HIS A 904 
 PHE   0.016   0.001   PHE A 828 
 TYR   0.010   0.001   TYR A 937 
 ARG   0.004   0.001   ARG A 847 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03686 (  148)
  hydrogen bonds       : angle       5.07264 (  438)
  SS BOND              : bond        0.00265 (   13)
  SS BOND              : angle       0.84267 (   26)
  covalent geometry    : bond        0.00317 ( 5372)
  covalent geometry    : angle       0.54929 ( 7270)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  753 ARG cc_start: 0.7088 (ptp-110) cc_final: 0.6844 (ptp-110)
REVERT: A  770 MET cc_start: 0.6662 (mmp) cc_final: 0.6306 (mmm)
REVERT: A  831 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7694 (ptpt)
REVERT: A  868 LEU cc_start: 0.8343 (tt) cc_final: 0.8076 (mp)
REVERT: B  908 GLN cc_start: 0.8251 (tp40) cc_final: 0.7975 (tp40)
REVERT: C  113 LYS cc_start: 0.7860 (tppp) cc_final: 0.7612 (tppp)
REVERT: C  130 TYR cc_start: 0.8147 (m-10) cc_final: 0.7834 (m-80)
  outliers start: 15
  outliers final: 14
  residues processed: 113
  average time/residue: 0.1729
  time to fit residues: 25.1343
Evaluate side-chains
  116 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  831 LYS
Chi-restraints excluded: chain A residue  836 VAL
Chi-restraints excluded: chain A residue  886 ASN
Chi-restraints excluded: chain A residue  930 SER
Chi-restraints excluded: chain A residue  951 ASP
Chi-restraints excluded: chain A residue 1006 CYS
Chi-restraints excluded: chain B residue  714 VAL
Chi-restraints excluded: chain B residue  764 ASN
Chi-restraints excluded: chain B residue  781 ASP
Chi-restraints excluded: chain B residue  864 ASN
Chi-restraints excluded: chain B residue  906 CYS
Chi-restraints excluded: chain B residue  972 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 69 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.3903 r_free = 0.3903 target = 0.138912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.115158 restraints weight = 8703.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 3.60
r_work: 0.3462 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5385  Z= 0.206
  Angle     :  0.612   9.621   7296  Z= 0.322
  Chirality :  0.047   0.162    753
  Planarity :  0.004   0.061    975
  Dihedral  :  4.755  27.569    768
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 15.59 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.30), residues: 726
  helix:  0.26 (0.51), residues: 109
  sheet: -0.82 (0.33), residues: 178
  loop : -1.08 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 814 
 HIS   0.005   0.001   HIS B 983 
 PHE   0.014   0.002   PHE B 828 
 TYR   0.013   0.002   TYR B 739 
 ARG   0.004   0.001   ARG A 847 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04132 (  148)
  hydrogen bonds       : angle       5.26417 (  438)
  SS BOND              : bond        0.00359 (   13)
  SS BOND              : angle       1.14344 (   26)
  covalent geometry    : bond        0.00443 ( 5372)
  covalent geometry    : angle       0.60926 ( 7270)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  868 LEU cc_start: 0.8371 (tt) cc_final: 0.8103 (mp)
REVERT: B  908 GLN cc_start: 0.8262 (tp40) cc_final: 0.7974 (tp40)
REVERT: C  113 LYS cc_start: 0.7889 (tppp) cc_final: 0.7612 (tppp)
REVERT: C  130 TYR cc_start: 0.8294 (m-10) cc_final: 0.7914 (m-80)
  outliers start: 17
  outliers final: 15
  residues processed: 114
  average time/residue: 0.1579
  time to fit residues: 24.1223
Evaluate side-chains
  117 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  831 LYS
Chi-restraints excluded: chain A residue  836 VAL
Chi-restraints excluded: chain A residue  886 ASN
Chi-restraints excluded: chain A residue  930 SER
Chi-restraints excluded: chain A residue  951 ASP
Chi-restraints excluded: chain A residue 1006 CYS
Chi-restraints excluded: chain B residue  712 VAL
Chi-restraints excluded: chain B residue  714 VAL
Chi-restraints excluded: chain B residue  781 ASP
Chi-restraints excluded: chain B residue  864 ASN
Chi-restraints excluded: chain B residue  906 CYS
Chi-restraints excluded: chain B residue  972 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 64 optimal weight:    0.0970
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3942 r_free = 0.3942 target = 0.141858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.118155 restraints weight = 8715.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 3.60
r_work: 0.3510 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5385  Z= 0.135
  Angle     :  0.582   8.522   7296  Z= 0.309
  Chirality :  0.046   0.200    753
  Planarity :  0.004   0.060    975
  Dihedral  :  4.612  27.672    768
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.97 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.30), residues: 726
  helix:  0.32 (0.51), residues: 109
  sheet: -0.76 (0.34), residues: 174
  loop : -1.09 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 814 
 HIS   0.003   0.001   HIS B 983 
 PHE   0.018   0.001   PHE A 828 
 TYR   0.010   0.001   TYR B 739 
 ARG   0.004   0.000   ARG A 847 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03772 (  148)
  hydrogen bonds       : angle       5.19609 (  438)
  SS BOND              : bond        0.00261 (   13)
  SS BOND              : angle       0.80804 (   26)
  covalent geometry    : bond        0.00293 ( 5372)
  covalent geometry    : angle       0.58119 ( 7270)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2718.52 seconds
wall clock time: 47 minutes 48.20 seconds (2868.20 seconds total)