Starting phenix.real_space_refine
on Sun Apr 27 09:43:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g5i_51087/04_2025/9g5i_51087_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g5i_51087/04_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_51087/04_2025/9g5i_51087.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g5i_51087/04_2025/9g5i_51087.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g5i_51087/04_2025/9g5i_51087_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g5i_51087/04_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-5669/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: 4.32, per 1000 atoms: 0.82
  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: 1.24
  Conformation dependent library (CDL) restraints added in 627.0 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: 0.58
  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: 1.42

  Time building geometry restraints manager: 1.49 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:             2.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.480
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.180
-------------------------------------------------------------------------------
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  : 0.588 
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: 0.1568
  time to fit residues: 23.7052
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  : 0.547 
-------------------------------------------------------------------------------
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 = 38)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.116178 restraints weight = 8944.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 3.62
r_work: 0.3447 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3447
-------------------------------------------------------------------------------
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  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  770 MET cc_start: 0.6892 (mmm) cc_final: 0.6682 (mmt)
REVERT: A  997 MET cc_start: 0.3498 (ttp) cc_final: 0.2787 (mtp)
REVERT: B  947 ASP cc_start: 0.8244 (t0) cc_final: 0.8026 (t70)
REVERT: C  113 LYS cc_start: 0.7748 (tppt) cc_final: 0.7511 (tppp)
REVERT: C  130 TYR cc_start: 0.7935 (m-10) cc_final: 0.7502 (m-80)
REVERT: C  132 LYS cc_start: 0.8338 (mmmm) cc_final: 0.8133 (mmtm)
  outliers start: 2
  outliers final: 1
  residues processed: 115
  average time/residue: 0.1591
  time to fit residues: 23.9111
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  : 0.514 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 59 optimal weight:    8.9990
   chunk 50 optimal weight:    0.4980
   chunk 6 optimal weight:    8.9990
   chunk 54 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.8988

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.138800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.114617 restraints weight = 8742.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 3.61
r_work: 0.3451 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5385  Z= 0.241
  Angle     :  0.611   7.721   7296  Z= 0.326
  Chirality :  0.048   0.168    753
  Planarity :  0.004   0.064    975
  Dihedral  :  4.885  26.534    768
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 10.27 %
    Favored  : 88.02 %
  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: -1.36 (0.29), residues: 726
  helix:  0.32 (0.52), residues: 109
  sheet: -1.00 (0.32), residues: 187
  loop : -1.17 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 814 
 HIS   0.004   0.001   HIS A 812 
 PHE   0.019   0.002   PHE A 828 
 TYR   0.014   0.002   TYR B 739 
 ARG   0.007   0.001   ARG C 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04703 (  148)
  hydrogen bonds       : angle       5.60151 (  438)
  SS BOND              : bond        0.00542 (   13)
  SS BOND              : angle       1.15353 (   26)
  covalent geometry    : bond        0.00517 ( 5372)
  covalent geometry    : angle       0.60822 ( 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: 9
    poor density    : 105
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  997 MET cc_start: 0.6623 (tpt) cc_final: 0.3790 (ptm)
REVERT: C  130 TYR cc_start: 0.8183 (m-10) cc_final: 0.7858 (m-80)
REVERT: C  132 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8288 (mmtm)
  outliers start: 9
  outliers final: 6
  residues processed: 108
  average time/residue: 0.1474
  time to fit residues: 21.3202
Evaluate side-chains
  103 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 B residue  714 VAL
Chi-restraints excluded: chain B residue  764 ASN
Chi-restraints excluded: chain B residue  781 ASP
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:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   overall best weight:    1.3388

-------------------------------------------------------------------------------
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 = 0.3920 r_free = 0.3920 target = 0.140006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.115840 restraints weight = 8868.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 3.67
r_work: 0.3470 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5385  Z= 0.182
  Angle     :  0.590  10.132   7296  Z= 0.307
  Chirality :  0.047   0.167    753
  Planarity :  0.004   0.063    975
  Dihedral  :  4.764  26.749    768
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 12.93 %
    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: -1.32 (0.29), residues: 726
  helix:  0.37 (0.52), residues: 109
  sheet: -0.83 (0.34), residues: 171
  loop : -1.23 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 814 
 HIS   0.003   0.001   HIS A 904 
 PHE   0.028   0.002   PHE C  97 
 TYR   0.011   0.001   TYR B 739 
 ARG   0.003   0.001   ARG C 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04177 (  148)
  hydrogen bonds       : angle       5.42113 (  438)
  SS BOND              : bond        0.00366 (   13)
  SS BOND              : angle       1.07663 (   26)
  covalent geometry    : bond        0.00388 ( 5372)
  covalent geometry    : angle       0.58726 ( 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
  120 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  947 ASP cc_start: 0.8263 (t0) cc_final: 0.8020 (t70)
REVERT: B  997 MET cc_start: 0.6732 (tpt) cc_final: 0.3729 (ptm)
REVERT: C  113 LYS cc_start: 0.7953 (tppp) cc_final: 0.7596 (tppp)
REVERT: C  130 TYR cc_start: 0.8187 (m-10) cc_final: 0.7914 (m-80)
  outliers start: 14
  outliers final: 12
  residues processed: 112
  average time/residue: 0.1442
  time to fit residues: 21.8964
Evaluate side-chains
  112 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
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  801 ILE
Chi-restraints excluded: chain B residue  972 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0010
   chunk 1 optimal weight:    0.1980
   chunk 21 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 43 optimal weight:    0.3980
   chunk 69 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.3986

-------------------------------------------------------------------------------
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
B 777 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.144308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.120307 restraints weight = 8628.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 3.61
r_work: 0.3542 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5385  Z= 0.107
  Angle     :  0.523   6.604   7296  Z= 0.272
  Chirality :  0.045   0.161    753
  Planarity :  0.004   0.060    975
  Dihedral  :  4.370  26.754    768
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 13.69 %
    Favored  : 83.46 %
  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:  0.53 (0.52), residues: 109
  sheet: -0.92 (0.33), residues: 192
  loop : -1.06 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 883 
 HIS   0.002   0.000   HIS A 904 
 PHE   0.018   0.001   PHE A 828 
 TYR   0.007   0.001   TYR C 119 
 ARG   0.003   0.000   ARG A 847 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03557 (  148)
  hydrogen bonds       : angle       5.11050 (  438)
  SS BOND              : bond        0.00257 (   13)
  SS BOND              : angle       0.68572 (   26)
  covalent geometry    : bond        0.00225 ( 5372)
  covalent geometry    : angle       0.52280 ( 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
  126 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  908 GLN cc_start: 0.8180 (tp40) cc_final: 0.7943 (tp40)
REVERT: B  947 ASP cc_start: 0.8240 (t0) cc_final: 0.8018 (t70)
REVERT: B  997 MET cc_start: 0.6529 (tpt) cc_final: 0.3699 (ptm)
REVERT: C  113 LYS cc_start: 0.7893 (tppp) cc_final: 0.7639 (tppp)
REVERT: C  130 TYR cc_start: 0.8086 (m-10) cc_final: 0.7758 (m-80)
  outliers start: 15
  outliers final: 10
  residues processed: 117
  average time/residue: 0.1574
  time to fit residues: 24.3284
Evaluate side-chains
  115 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 61 optimal weight:    0.1980
   chunk 4 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 47 optimal weight:    7.9990
   chunk 17 optimal weight:   10.0000
   chunk 23 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   chunk 51 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.3961 r_free = 0.3961 target = 0.143231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.119409 restraints weight = 8692.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 3.63
r_work: 0.3533 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.1927

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= 0.120
  Angle     :  0.528   6.709   7296  Z= 0.275
  Chirality :  0.045   0.159    753
  Planarity :  0.004   0.059    975
  Dihedral  :  4.314  26.974    768
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 14.45 %
    Favored  : 83.27 %
  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: -1.17 (0.30), residues: 726
  helix:  0.43 (0.51), residues: 109
  sheet: -0.88 (0.33), residues: 189
  loop : -1.02 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 814 
 HIS   0.002   0.001   HIS A 904 
 PHE   0.016   0.001   PHE A 828 
 TYR   0.008   0.001   TYR C 131 
 ARG   0.003   0.000   ARG A 847 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03593 (  148)
  hydrogen bonds       : angle       5.08395 (  438)
  SS BOND              : bond        0.00264 (   13)
  SS BOND              : angle       0.66424 (   26)
  covalent geometry    : bond        0.00257 ( 5372)
  covalent geometry    : angle       0.52722 ( 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
  118 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  770 MET cc_start: 0.6500 (mmp) cc_final: 0.5725 (mmm)
REVERT: A  868 LEU cc_start: 0.8327 (tt) cc_final: 0.8025 (mp)
REVERT: B  908 GLN cc_start: 0.8183 (tp40) cc_final: 0.7906 (tp40)
REVERT: B  974 GLU cc_start: 0.7461 (pt0) cc_final: 0.7248 (pt0)
REVERT: B  997 MET cc_start: 0.6550 (tpt) cc_final: 0.3707 (ptm)
REVERT: C  113 LYS cc_start: 0.7884 (tppp) cc_final: 0.7651 (tppp)
REVERT: C  130 TYR cc_start: 0.8043 (m-10) cc_final: 0.7731 (m-80)
  outliers start: 12
  outliers final: 11
  residues processed: 111
  average time/residue: 0.1601
  time to fit residues: 23.5549
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  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 B residue  781 ASP
Chi-restraints excluded: chain B residue  801 ILE
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:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3934 r_free = 0.3934 target = 0.141163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.117251 restraints weight = 8638.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 3.60
r_work: 0.3500 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.1997

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= 0.160
  Angle     :  0.555   7.132   7296  Z= 0.291
  Chirality :  0.046   0.160    753
  Planarity :  0.004   0.060    975
  Dihedral  :  4.452  27.069    768
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 14.45 %
    Favored  : 82.70 %
  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: -1.17 (0.30), residues: 726
  helix:  0.42 (0.51), residues: 109
  sheet: -0.87 (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   0.003   0.001   HIS A 812 
 PHE   0.017   0.002   PHE A 828 
 TYR   0.011   0.001   TYR B 739 
 ARG   0.003   0.001   ARG A 847 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03823 (  148)
  hydrogen bonds       : angle       5.14104 (  438)
  SS BOND              : bond        0.00298 (   13)
  SS BOND              : angle       0.85157 (   26)
  covalent geometry    : bond        0.00343 ( 5372)
  covalent geometry    : angle       0.55345 ( 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
  118 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  868 LEU cc_start: 0.8381 (tt) cc_final: 0.8100 (mp)
REVERT: B  908 GLN cc_start: 0.8227 (tp40) cc_final: 0.7947 (tp40)
REVERT: B  947 ASP cc_start: 0.8243 (t0) cc_final: 0.8022 (t70)
REVERT: B  997 MET cc_start: 0.6600 (tpt) cc_final: 0.3660 (ptm)
REVERT: C  113 LYS cc_start: 0.7889 (tppp) cc_final: 0.7637 (tppp)
REVERT: C  130 TYR cc_start: 0.8137 (m-10) cc_final: 0.7816 (m-80)
  outliers start: 15
  outliers final: 13
  residues processed: 110
  average time/residue: 0.1547
  time to fit residues: 22.8390
Evaluate side-chains
  114 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  733 THR
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  801 ILE
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:    0.8980
   chunk 53 optimal weight:    7.9990
   chunk 64 optimal weight:    2.9990
   chunk 4 optimal weight:    0.4980
   chunk 16 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0470
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.5678

-------------------------------------------------------------------------------
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 = 0.3963 r_free = 0.3963 target = 0.143219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.119625 restraints weight = 8544.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 3.56
r_work: 0.3539 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5385  Z= 0.114
  Angle     :  0.534   7.587   7296  Z= 0.278
  Chirality :  0.045   0.160    753
  Planarity :  0.004   0.060    975
  Dihedral  :  4.304  27.180    768
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.02 %
    Favored  : 82.32 %
  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:  0.41 (0.51), residues: 109
  sheet: -0.80 (0.34), residues: 177
  loop : -1.01 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 814 
 HIS   0.002   0.000   HIS A 904 
 PHE   0.010   0.001   PHE A 828 
 TYR   0.008   0.001   TYR B 739 
 ARG   0.003   0.000   ARG A 847 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03492 (  148)
  hydrogen bonds       : angle       5.01411 (  438)
  SS BOND              : bond        0.00242 (   13)
  SS BOND              : angle       0.59895 (   26)
  covalent geometry    : bond        0.00242 ( 5372)
  covalent geometry    : angle       0.53388 ( 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
  116 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  908 GLN cc_start: 0.8219 (tp40) cc_final: 0.7934 (tp40)
REVERT: B  947 ASP cc_start: 0.8249 (t0) cc_final: 0.8024 (t70)
REVERT: B  974 GLU cc_start: 0.7481 (pt0) cc_final: 0.7273 (pt0)
REVERT: B  997 MET cc_start: 0.6475 (tpt) cc_final: 0.3599 (ptm)
REVERT: C  113 LYS cc_start: 0.7879 (tppp) cc_final: 0.7678 (tppp)
REVERT: C  130 TYR cc_start: 0.8044 (m-10) cc_final: 0.7706 (m-80)
  outliers start: 14
  outliers final: 13
  residues processed: 107
  average time/residue: 0.1744
  time to fit residues: 24.9206
Evaluate side-chains
  113 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  733 THR
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  731 THR
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:    0.0370
   chunk 19 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.6858

-------------------------------------------------------------------------------
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 = 0.3960 r_free = 0.3960 target = 0.143034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.119336 restraints weight = 8624.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 3.60
r_work: 0.3533 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.2142

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= 0.123
  Angle     :  0.533   7.740   7296  Z= 0.279
  Chirality :  0.045   0.157    753
  Planarity :  0.004   0.059    975
  Dihedral  :  4.272  27.315    768
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.02 %
    Favored  : 82.32 %
  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: -1.10 (0.30), residues: 726
  helix:  0.42 (0.51), residues: 109
  sheet: -0.78 (0.33), residues: 186
  loop : -1.00 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 814 
 HIS   0.002   0.001   HIS A 904 
 PHE   0.014   0.001   PHE A 828 
 TYR   0.009   0.001   TYR B 739 
 ARG   0.004   0.001   ARG A 847 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03533 (  148)
  hydrogen bonds       : angle       5.01646 (  438)
  SS BOND              : bond        0.00246 (   13)
  SS BOND              : angle       0.64587 (   26)
  covalent geometry    : bond        0.00262 ( 5372)
  covalent geometry    : angle       0.53273 ( 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: 14
    poor density    : 107
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  886 ASN cc_start: 0.7209 (m-40) cc_final: 0.6978 (t0)
REVERT: B  908 GLN cc_start: 0.8214 (tp40) cc_final: 0.7941 (tp40)
REVERT: B  947 ASP cc_start: 0.8253 (t0) cc_final: 0.8019 (t70)
REVERT: C  113 LYS cc_start: 0.7866 (tppp) cc_final: 0.7655 (tppp)
REVERT: C  130 TYR cc_start: 0.8021 (m-10) cc_final: 0.7672 (m-80)
  outliers start: 14
  outliers final: 14
  residues processed: 112
  average time/residue: 0.1605
  time to fit residues: 23.7527
Evaluate side-chains
  118 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
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  731 THR
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:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0970
   chunk 3 optimal weight:    0.8980
   overall best weight:    1.5984

-------------------------------------------------------------------------------
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 = 0.3904 r_free = 0.3904 target = 0.138933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.115419 restraints weight = 8722.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 3.54
r_work: 0.3468 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5385  Z= 0.205
  Angle     :  0.597   9.358   7296  Z= 0.314
  Chirality :  0.047   0.161    753
  Planarity :  0.004   0.060    975
  Dihedral  :  4.626  27.437    768
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.40 %
    Favored  : 81.94 %
  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:  0.30 (0.51), residues: 109
  sheet: -0.94 (0.33), residues: 187
  loop : -1.03 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 814 
 HIS   0.003   0.001   HIS A 812 
 PHE   0.013   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        0.04101 (  148)
  hydrogen bonds       : angle       5.26059 (  438)
  SS BOND              : bond        0.00355 (   13)
  SS BOND              : angle       1.04141 (   26)
  covalent geometry    : bond        0.00435 ( 5372)
  covalent geometry    : angle       0.59508 ( 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
  125 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  753 ARG cc_start: 0.7235 (ptp-110) cc_final: 0.6866 (ptp-110)
REVERT: B  734 TYR cc_start: 0.8313 (m-80) cc_final: 0.8068 (m-80)
REVERT: B  908 GLN cc_start: 0.8276 (tp40) cc_final: 0.7982 (tp40)
REVERT: B  947 ASP cc_start: 0.8285 (t0) cc_final: 0.8029 (t70)
REVERT: C  106 TYR cc_start: 0.6859 (t80) cc_final: 0.6566 (t80)
REVERT: C  113 LYS cc_start: 0.7942 (tppp) cc_final: 0.7669 (tppp)
REVERT: C  130 TYR cc_start: 0.8211 (m-10) cc_final: 0.7849 (m-80)
  outliers start: 14
  outliers final: 14
  residues processed: 118
  average time/residue: 0.1776
  time to fit residues: 27.1409
Evaluate side-chains
  119 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  731 THR
Chi-restraints excluded: chain B residue  781 ASP
Chi-restraints excluded: chain B residue  801 ILE
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:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 53 optimal weight:    6.9990
   chunk 64 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3941 r_free = 0.3941 target = 0.141669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.117998 restraints weight = 8729.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 3.60
r_work: 0.3513 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.2214

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= 0.134
  Angle     :  0.557   7.795   7296  Z= 0.292
  Chirality :  0.046   0.163    753
  Planarity :  0.004   0.060    975
  Dihedral  :  4.477  27.441    768
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.97 %
    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: -1.13 (0.30), residues: 726
  helix:  0.32 (0.51), residues: 109
  sheet: -0.75 (0.35), residues: 172
  loop : -1.01 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 814 
 HIS   0.002   0.001   HIS A 812 
 PHE   0.010   0.001   PHE A 828 
 TYR   0.009   0.001   TYR B 739 
 ARG   0.004   0.001   ARG A 847 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03649 (  148)
  hydrogen bonds       : angle       5.12178 (  438)
  SS BOND              : bond        0.00262 (   13)
  SS BOND              : angle       0.91240 (   26)
  covalent geometry    : bond        0.00288 ( 5372)
  covalent geometry    : angle       0.55540 ( 7270)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2601.51 seconds
wall clock time: 45 minutes 35.04 seconds (2735.04 seconds total)