Starting phenix.real_space_refine
on Fri Aug 22 20:44:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xh7_38343/08_2025/8xh7_38343.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xh7_38343/08_2025/8xh7_38343.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xh7_38343/08_2025/8xh7_38343.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xh7_38343/08_2025/8xh7_38343.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xh7_38343/08_2025/8xh7_38343.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xh7_38343/08_2025/8xh7_38343.cif"
  }
  resolution = 3.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.006
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      42      5.16       5
     C    5610      2.51       5
     N    1134      2.21       5
     O    1116      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7902
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1317
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 1, 'TRANS': 159}
    Chain: "E"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1317
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 1, 'TRANS': 159}
    Chain: "F"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1317
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 1, 'TRANS': 159}
    Chain: "A"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1317
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 1, 'TRANS': 159}
    Chain: "B"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1317
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 1, 'TRANS': 159}
    Chain: "D"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1317
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 1, 'TRANS': 159}
  Time building chain proxies: 2.18, per 1000 atoms: 0.28
  Number of scatterers: 7902
  At special positions: 0
  Unit cell: (125.32, 109.2, 60.32, 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      42     16.00
     O    1116      8.00
     N    1134      7.00
     C    5610      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 520.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1800

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 0 sheets defined
      90.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'C' and resid 24 through 45
    Processing helix  chain 'C' and resid 51 through 72
      removed outlier: 3.932A  pdb=" N   LEU C  55 " --> pdb=" O   ALA C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 77
    Processing helix  chain 'C' and resid 78 through 99
      removed outlier: 4.659A  pdb=" N   ASN C  99 " --> pdb=" O   ILE C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 134
    Processing helix  chain 'C' and resid 136 through 160
    Processing helix  chain 'C' and resid 162 through 180
      removed outlier: 3.612A  pdb=" N   LEU C 168 " --> pdb=" O   TRP C 164 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE C 180 " --> pdb=" O   LEU C 176 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 25 through 44
      removed outlier: 3.826A  pdb=" N   MET E  44 " --> pdb=" O   LEU E  40 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 50 through 72
      removed outlier: 3.926A  pdb=" N   VAL E  54 " --> pdb=" O   GLY E  50 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 79 through 98
      removed outlier: 3.793A  pdb=" N   LEU E  83 " --> pdb=" O   PRO E  79 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 103 through 134
      removed outlier: 3.636A  pdb=" N   LEU E 107 " --> pdb=" O   GLN E 103 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 136 through 160
      removed outlier: 3.550A  pdb=" N   TYR E 159 " --> pdb=" O   ILE E 155 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 164 through 184
      removed outlier: 3.545A  pdb=" N   LEU E 168 " --> pdb=" O   TRP E 164 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   MET E 184 " --> pdb=" O   ILE E 180 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 44
      removed outlier: 3.757A  pdb=" N   MET F  44 " --> pdb=" O   LEU F  40 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 50 through 73
      removed outlier: 3.800A  pdb=" N   VAL F  54 " --> pdb=" O   GLY F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 74 through 77
      removed outlier: 3.898A  pdb=" N   LEU F  77 " --> pdb=" O   ARG F  74 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 74 through 77'
    Processing helix  chain 'F' and resid 78 through 100
      removed outlier: 3.535A  pdb=" N   GLY F  82 " --> pdb=" O   CYS F  78 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ASN F  99 " --> pdb=" O   ILE F  95 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU F 100 " --> pdb=" O   ALA F  96 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 134
    Processing helix  chain 'F' and resid 136 through 160
    Processing helix  chain 'F' and resid 162 through 180
    Processing helix  chain 'A' and resid 25 through 44
      removed outlier: 3.852A  pdb=" N   MET A  44 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 72
      removed outlier: 3.926A  pdb=" N   VAL A  54 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 98
      removed outlier: 3.774A  pdb=" N   LEU A  83 " --> pdb=" O   PRO A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 134
      removed outlier: 3.665A  pdb=" N   LEU A 107 " --> pdb=" O   GLN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 160
      removed outlier: 3.557A  pdb=" N   TYR A 159 " --> pdb=" O   ILE A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 184
      removed outlier: 3.552A  pdb=" N   LEU A 168 " --> pdb=" O   TRP A 164 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   MET A 184 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 44
      removed outlier: 3.502A  pdb=" N   MET B  44 " --> pdb=" O   LEU B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 73
      removed outlier: 3.808A  pdb=" N   VAL B  54 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 77
      removed outlier: 3.883A  pdb=" N   LEU B  77 " --> pdb=" O   ARG B  74 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 74 through 77'
    Processing helix  chain 'B' and resid 78 through 100
      removed outlier: 3.540A  pdb=" N   GLY B  82 " --> pdb=" O   CYS B  78 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   ASN B  99 " --> pdb=" O   ILE B  95 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU B 100 " --> pdb=" O   ALA B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 134
    Processing helix  chain 'B' and resid 136 through 160
    Processing helix  chain 'B' and resid 162 through 180
    Processing helix  chain 'D' and resid 25 through 45
    Processing helix  chain 'D' and resid 51 through 72
      removed outlier: 3.869A  pdb=" N   LEU D  55 " --> pdb=" O   ALA D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 77
    Processing helix  chain 'D' and resid 78 through 99
      removed outlier: 4.645A  pdb=" N   ASN D  99 " --> pdb=" O   ILE D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 134
    Processing helix  chain 'D' and resid 136 through 160
    Processing helix  chain 'D' and resid 162 through 180
      removed outlier: 3.655A  pdb=" N   LEU D 168 " --> pdb=" O   TRP D 164 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE D 180 " --> pdb=" O   LEU D 176 " (cutoff:3.500A)

    683 hydrogen bonds defined for protein.
    2037 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: 1.23

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1044
        1.29 -     1.43: 2259
        1.43 -     1.57: 4749
        1.57 -     1.70: 0
        1.70 -     1.84: 72
  Bond restraints: 8124
  Sorted by residual:
  bond pdb=" C   MET A  61 "
       pdb=" O   MET A  61 "
    ideal  model  delta    sigma   weight residual
    1.237  1.157  0.080 1.17e-02 7.31e+03 4.66e+01
  bond pdb=" N   ILE E  64 "
       pdb=" CA  ILE E  64 "
    ideal  model  delta    sigma   weight residual
    1.461  1.500 -0.039 1.17e-02 7.31e+03 1.10e+01
  bond pdb=" N   ILE A  64 "
       pdb=" CA  ILE A  64 "
    ideal  model  delta    sigma   weight residual
    1.461  1.500 -0.039 1.17e-02 7.31e+03 1.09e+01
  bond pdb=" N   LEU B 181 "
       pdb=" CA  LEU B 181 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.29e-02 6.01e+03 1.06e+01
  bond pdb=" N   ILE D  69 "
       pdb=" CA  ILE D  69 "
    ideal  model  delta    sigma   weight residual
    1.461  1.499 -0.038 1.19e-02 7.06e+03 1.04e+01
  ... (remaining 8119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 10134
        1.46 -     2.91: 754
        2.91 -     4.37: 170
        4.37 -     5.83: 53
        5.83 -     7.29: 13
  Bond angle restraints: 11124
  Sorted by residual:
  angle pdb=" CA  MET A  61 "
        pdb=" C   MET A  61 "
        pdb=" O   MET A  61 "
      ideal   model   delta    sigma   weight residual
     120.55  113.26    7.29 1.06e+00 8.90e-01 4.72e+01
  angle pdb=" CA  ILE C 180 "
        pdb=" C   ILE C 180 "
        pdb=" O   ILE C 180 "
      ideal   model   delta    sigma   weight residual
     122.13  116.43    5.70 1.11e+00 8.12e-01 2.64e+01
  angle pdb=" C   ALA F  59 "
        pdb=" N   LEU F  60 "
        pdb=" CA  LEU F  60 "
      ideal   model   delta    sigma   weight residual
     120.31  113.36    6.95 1.52e+00 4.33e-01 2.09e+01
  angle pdb=" O   LEU C  60 "
        pdb=" C   LEU C  60 "
        pdb=" N   MET C  61 "
      ideal   model   delta    sigma   weight residual
     122.12  126.81   -4.69 1.06e+00 8.90e-01 1.96e+01
  angle pdb=" N   MET A  61 "
        pdb=" CA  MET A  61 "
        pdb=" C   MET A  61 "
      ideal   model   delta    sigma   weight residual
     111.28  106.48    4.80 1.09e+00 8.42e-01 1.94e+01
  ... (remaining 11119 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.11: 3883
       16.11 -    32.22: 436
       32.22 -    48.33: 139
       48.33 -    64.44: 22
       64.44 -    80.55: 2
  Dihedral angle restraints: 4482
    sinusoidal: 1692
      harmonic: 2790
  Sorted by residual:
  dihedral pdb=" C   ILE A  71 "
           pdb=" N   ILE A  71 "
           pdb=" CA  ILE A  71 "
           pdb=" CB  ILE A  71 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.43    8.43     0      2.50e+00 1.60e-01 1.14e+01
  dihedral pdb=" CA  ASP B  75 "
           pdb=" CB  ASP B  75 "
           pdb=" CG  ASP B  75 "
           pdb=" OD1 ASP B  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.90   56.90     1      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CA  ASP F  75 "
           pdb=" CB  ASP F  75 "
           pdb=" CG  ASP F  75 "
           pdb=" OD1 ASP F  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.88   56.88     1      2.00e+01 2.50e-03 1.09e+01
  ... (remaining 4479 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1180
       0.067 -    0.134: 146
       0.134 -    0.201: 61
       0.201 -    0.268: 28
       0.268 -    0.335: 7
  Chirality restraints: 1422
  Sorted by residual:
  chirality pdb=" CA  ILE E  64 "
            pdb=" N   ILE E  64 "
            pdb=" C   ILE E  64 "
            pdb=" CB  ILE E  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.77   -0.34 2.00e-01 2.50e+01 2.81e+00
  chirality pdb=" CA  ILE A  64 "
            pdb=" N   ILE A  64 "
            pdb=" C   ILE A  64 "
            pdb=" CB  ILE A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.74   -0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CA  LEU B  88 "
            pdb=" N   LEU B  88 "
            pdb=" C   LEU B  88 "
            pdb=" CB  LEU B  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.98e+00
  ... (remaining 1419 not shown)

  Planarity restraints: 1206
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  47 "   -0.019 2.00e-02 2.50e+03   1.19e-02 3.53e+00
        pdb=" CG  TRP A  47 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  47 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  47 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  47 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 153 "   -0.009 2.00e-02 2.50e+03   1.86e-02 3.47e+00
        pdb=" C   LEU E 153 "    0.032 2.00e-02 2.50e+03
        pdb=" O   LEU E 153 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LEU E 154 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  62 "   -0.008 2.00e-02 2.50e+03   1.74e-02 3.02e+00
        pdb=" C   LEU A  62 "    0.030 2.00e-02 2.50e+03
        pdb=" O   LEU A  62 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ILE A  63 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1203 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 2753
        2.88 -     3.39: 8491
        3.39 -     3.89: 13348
        3.89 -     4.40: 14230
        4.40 -     4.90: 23282
  Nonbonded interactions: 62104
  Sorted by model distance:
  nonbonded pdb=" O   TRP C  47 "
            pdb=" OG1 THR C  48 "
     model   vdw
     2.376 3.040
  nonbonded pdb=" O   TRP D  47 "
            pdb=" OG1 THR D  48 "
     model   vdw
     2.393 3.040
  nonbonded pdb=" NH1 ARG F  73 "
            pdb=" O   MET F 184 "
     model   vdw
     2.397 3.120
  nonbonded pdb=" O   LEU F 154 "
            pdb=" CD1 LEU F 158 "
     model   vdw
     2.414 3.460
  nonbonded pdb=" O   TRP F  47 "
            pdb=" OG1 THR F  48 "
     model   vdw
     2.460 3.040
  ... (remaining 62099 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             15.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.340
  Find NCS groups from input model:        0.130
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
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      :  0.005   0.080   8124  Z= 0.388
  Angle     :  0.913   7.286  11124  Z= 0.631
  Chirality :  0.065   0.335   1422
  Planarity :  0.003   0.021   1206
  Dihedral  : 14.929  80.553   2682
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  4.59 %
    Favored  : 93.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.45 (0.27), residues: 954
  helix:  2.03 (0.17), residues: 864
  sheet:  None (None), residues: 0
  loop : -2.55 (0.55), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  73 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.018   0.001   PHE D  58 
 TRP   0.031   0.001   TRP A  47 
 HIS   0.000   0.000   HIS D 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 ( 8124)
  covalent geometry    : angle       0.91266 (11124)
  hydrogen bonds       : bond        0.09805 (  683)
  hydrogen bonds       : angle       4.50594 ( 2037)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 197
  time to evaluate  : 0.280 
Fit side-chains
REVERT: C   40 LEU cc_start: 0.8526 (tp) cc_final: 0.8214 (tp)
REVERT: C   44 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7694 (mpp)
REVERT: F  140 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.7018 (mp)
REVERT: A  178 MET cc_start: 0.6683 (tpp) cc_final: 0.6433 (mmt)
REVERT: B  165 TRP cc_start: 0.7807 (t-100) cc_final: 0.7548 (t-100)
  outliers start: 18
  outliers final: 7
  residues processed: 206
  average time/residue: 0.0575
  time to fit residues: 18.0146
Evaluate side-chains
  165 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 156
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain E residue   42 ILE
Chi-restraints excluded: chain F residue  129 ILE
Chi-restraints excluded: chain F residue  140 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  158 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0470
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
F 139 GLN
B 139 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.208034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.179260 restraints weight = 9005.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.180761 restraints weight = 7136.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.182020 restraints weight = 6248.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.182319 restraints weight = 5735.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.182319 restraints weight = 5536.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.1416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8124  Z= 0.134
  Angle     :  0.582  10.441  11124  Z= 0.273
  Chirality :  0.035   0.163   1422
  Planarity :  0.003   0.023   1206
  Dihedral  :  5.107  47.866   1027
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.91 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.23 (0.27), residues: 954
  helix:  2.52 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.87 (0.59), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 132 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.010   0.001   PHE D 112 
 TRP   0.011   0.001   TRP F 164 
 HIS   0.007   0.002   HIS F 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8124)
  covalent geometry    : angle       0.58191 (11124)
  hydrogen bonds       : bond        0.03503 (  683)
  hydrogen bonds       : angle       3.44854 ( 2037)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 0.252 
Fit side-chains
REVERT: C   44 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7784 (mtp)
REVERT: B  165 TRP cc_start: 0.7976 (t-100) cc_final: 0.7460 (t-100)
  outliers start: 20
  outliers final: 9
  residues processed: 170
  average time/residue: 0.0575
  time to fit residues: 15.2592
Evaluate side-chains
  156 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 146
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain F residue  139 GLN
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  144 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 63 optimal weight:    5.9990
   chunk 81 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 59 optimal weight:    8.9990
   chunk 5 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
F 101 HIS
F 139 GLN
B 101 HIS
B 139 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.215692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.177752 restraints weight = 9698.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.181130 restraints weight = 6569.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.183236 restraints weight = 5242.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.184105 restraints weight = 4592.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.184529 restraints weight = 4298.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.4337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8124  Z= 0.138
  Angle     :  0.566  11.137  11124  Z= 0.265
  Chirality :  0.034   0.186   1422
  Planarity :  0.002   0.024   1206
  Dihedral  :  4.578  52.998   1013
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 18.12 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.31 (0.27), residues: 954
  helix:  2.58 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.89 (0.61), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 132 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.009   0.001   PHE E 112 
 TRP   0.008   0.001   TRP A 131 
 HIS   0.005   0.001   HIS F 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8124)
  covalent geometry    : angle       0.56617 (11124)
  hydrogen bonds       : bond        0.03437 (  683)
  hydrogen bonds       : angle       3.35752 ( 2037)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 0.291 
Fit side-chains
REVERT: C  113 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8392 (mp)
REVERT: E  131 TRP cc_start: 0.8317 (t-100) cc_final: 0.8068 (t-100)
REVERT: F  155 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8586 (mt)
REVERT: B  155 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8596 (mt)
REVERT: D  113 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8391 (mp)
  outliers start: 25
  outliers final: 19
  residues processed: 164
  average time/residue: 0.0587
  time to fit residues: 14.8012
Evaluate side-chains
  171 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  139 GLN
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain B residue   98 TRP
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  144 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 85 optimal weight:    9.9990
   chunk 87 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 73 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
F 139 GLN
B 139 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.214441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.176098 restraints weight = 9813.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.179334 restraints weight = 6707.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.181605 restraints weight = 5357.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.182521 restraints weight = 4668.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.183036 restraints weight = 4353.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.4320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8124  Z= 0.141
  Angle     :  0.563  10.992  11124  Z= 0.263
  Chirality :  0.034   0.163   1422
  Planarity :  0.002   0.023   1206
  Dihedral  :  4.639  56.439   1013
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 21.01 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.40 (0.27), residues: 954
  helix:  2.63 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.78 (0.64), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  74 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.010   0.001   PHE E 112 
 TRP   0.007   0.001   TRP A 131 
 HIS   0.001   0.000   HIS D 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8124)
  covalent geometry    : angle       0.56343 (11124)
  hydrogen bonds       : bond        0.03413 (  683)
  hydrogen bonds       : angle       3.30244 ( 2037)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 152
  time to evaluate  : 0.173 
Fit side-chains
REVERT: C  113 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8341 (mp)
REVERT: F  113 ILE cc_start: 0.8192 (tp) cc_final: 0.7669 (pt)
REVERT: F  155 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8553 (mt)
REVERT: B  113 ILE cc_start: 0.8179 (tp) cc_final: 0.7694 (pt)
REVERT: B  155 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8567 (mt)
REVERT: D  113 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8348 (mp)
  outliers start: 34
  outliers final: 24
  residues processed: 172
  average time/residue: 0.0542
  time to fit residues: 14.4080
Evaluate side-chains
  176 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  139 GLN
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain F residue  181 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   98 TRP
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  144 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 75 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 85 optimal weight:   20.0000
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
F 139 GLN
B 139 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.211928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.174129 restraints weight = 9833.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.177522 restraints weight = 6640.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.179603 restraints weight = 5259.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.180583 restraints weight = 4596.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.180583 restraints weight = 4275.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.4298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8124  Z= 0.159
  Angle     :  0.586  10.775  11124  Z= 0.273
  Chirality :  0.035   0.167   1422
  Planarity :  0.002   0.023   1206
  Dihedral  :  4.710  56.543   1013
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 21.74 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.35 (0.27), residues: 954
  helix:  2.60 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.72 (0.67), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  74 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.011   0.001   PHE E 112 
 TRP   0.006   0.001   TRP F 164 
 HIS   0.001   0.000   HIS D 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 8124)
  covalent geometry    : angle       0.58623 (11124)
  hydrogen bonds       : bond        0.03535 (  683)
  hydrogen bonds       : angle       3.33758 ( 2037)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 150
  time to evaluate  : 0.280 
Fit side-chains
REVERT: C  113 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8369 (mp)
REVERT: C  158 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7480 (mm)
REVERT: F  113 ILE cc_start: 0.8145 (tp) cc_final: 0.7655 (pt)
REVERT: F  155 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8577 (mt)
REVERT: B  113 ILE cc_start: 0.8155 (tp) cc_final: 0.7685 (pt)
REVERT: B  155 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8600 (mt)
REVERT: D  113 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8387 (mp)
REVERT: D  158 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7456 (mm)
  outliers start: 41
  outliers final: 25
  residues processed: 174
  average time/residue: 0.0576
  time to fit residues: 15.3791
Evaluate side-chains
  179 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 148
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain F residue  181 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   98 TRP
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  143 PHE
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  129 ILE
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain D residue  158 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 83 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 95 optimal weight:    0.7980
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
F 101 HIS
B 101 HIS
B 139 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.205805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.174943 restraints weight = 9028.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.175461 restraints weight = 7011.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.177172 restraints weight = 6190.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.177557 restraints weight = 5658.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.177603 restraints weight = 5032.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8124  Z= 0.132
  Angle     :  0.573  10.300  11124  Z= 0.264
  Chirality :  0.034   0.167   1422
  Planarity :  0.002   0.022   1206
  Dihedral  :  4.633  55.938   1013
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 23.31 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.47 (0.27), residues: 954
  helix:  2.67 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.61 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  73 
 TYR   0.009   0.001   TYR D  41 
 PHE   0.008   0.001   PHE E 112 
 TRP   0.007   0.001   TRP F 164 
 HIS   0.005   0.001   HIS F 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8124)
  covalent geometry    : angle       0.57290 (11124)
  hydrogen bonds       : bond        0.03352 (  683)
  hydrogen bonds       : angle       3.23368 ( 2037)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 156
  time to evaluate  : 0.314 
Fit side-chains
REVERT: C  113 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8518 (mp)
REVERT: E   94 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7439 (tt)
REVERT: F  113 ILE cc_start: 0.8070 (tp) cc_final: 0.7678 (pt)
REVERT: F  155 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8736 (mt)
REVERT: A   94 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7381 (tt)
REVERT: B  113 ILE cc_start: 0.8087 (tp) cc_final: 0.7722 (pt)
REVERT: B  155 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8744 (mt)
REVERT: D   44 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7373 (mpp)
REVERT: D  113 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8498 (mp)
  outliers start: 37
  outliers final: 26
  residues processed: 175
  average time/residue: 0.0597
  time to fit residues: 15.8605
Evaluate side-chains
  188 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 155
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue   94 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  184 MET
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain F residue  181 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   98 TRP
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  143 PHE
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  144 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 43 optimal weight:   10.0000
   chunk 54 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.204329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.175357 restraints weight = 8985.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.174461 restraints weight = 8332.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.174964 restraints weight = 7768.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.175295 restraints weight = 7122.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.175672 restraints weight = 6588.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8124  Z= 0.137
  Angle     :  0.574   9.895  11124  Z= 0.267
  Chirality :  0.034   0.177   1422
  Planarity :  0.002   0.022   1206
  Dihedral  :  4.614  54.962   1013
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 22.58 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.47 (0.27), residues: 954
  helix:  2.67 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.62 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  73 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.009   0.001   PHE E 112 
 TRP   0.007   0.001   TRP F 164 
 HIS   0.001   0.000   HIS C 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8124)
  covalent geometry    : angle       0.57384 (11124)
  hydrogen bonds       : bond        0.03399 (  683)
  hydrogen bonds       : angle       3.24097 ( 2037)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 159
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: C  113 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8524 (mp)
REVERT: C  158 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7595 (mm)
REVERT: E   94 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7422 (tt)
REVERT: F  113 ILE cc_start: 0.8054 (tp) cc_final: 0.7669 (pt)
REVERT: F  155 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8739 (mt)
REVERT: A   94 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7357 (tt)
REVERT: B  113 ILE cc_start: 0.8087 (tp) cc_final: 0.7712 (pt)
REVERT: B  155 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8754 (mt)
REVERT: D   44 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.7406 (mpp)
REVERT: D  113 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8486 (mp)
REVERT: D  158 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7564 (mm)
  outliers start: 40
  outliers final: 26
  residues processed: 178
  average time/residue: 0.0607
  time to fit residues: 16.5689
Evaluate side-chains
  189 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 154
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue   94 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  184 MET
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain F residue  181 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   98 TRP
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  143 PHE
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  129 ILE
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain D residue  158 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0470
   chunk 30 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
B 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.214010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.176230 restraints weight = 9775.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.179756 restraints weight = 6581.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.181781 restraints weight = 5174.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.183161 restraints weight = 4527.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.183717 restraints weight = 4158.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.4333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8124  Z= 0.125
  Angle     :  0.564   9.876  11124  Z= 0.261
  Chirality :  0.034   0.181   1422
  Planarity :  0.002   0.022   1206
  Dihedral  :  4.569  54.727   1013
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 23.07 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.56 (0.27), residues: 954
  helix:  2.72 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.56 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  73 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.008   0.001   PHE D  58 
 TRP   0.007   0.001   TRP F 164 
 HIS   0.001   0.000   HIS C 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8124)
  covalent geometry    : angle       0.56406 (11124)
  hydrogen bonds       : bond        0.03286 (  683)
  hydrogen bonds       : angle       3.17427 ( 2037)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 160
  time to evaluate  : 0.222 
Fit side-chains
REVERT: C  113 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8304 (mp)
REVERT: C  158 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7395 (mm)
REVERT: E   94 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7290 (tt)
REVERT: F  113 ILE cc_start: 0.8023 (tp) cc_final: 0.7574 (pt)
REVERT: F  155 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8567 (mt)
REVERT: A   94 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7230 (tt)
REVERT: B  113 ILE cc_start: 0.8070 (tp) cc_final: 0.7631 (pt)
REVERT: B  155 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8590 (mt)
REVERT: D   44 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7431 (mpp)
REVERT: D  113 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8311 (mp)
REVERT: D  158 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7420 (mm)
  outliers start: 38
  outliers final: 25
  residues processed: 178
  average time/residue: 0.0580
  time to fit residues: 16.0014
Evaluate side-chains
  190 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 156
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue   94 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  184 MET
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain F residue  181 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   98 TRP
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain D residue  158 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.213047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.175366 restraints weight = 9772.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.178844 restraints weight = 6528.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.180871 restraints weight = 5151.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.182232 restraints weight = 4495.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.182608 restraints weight = 4147.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.4321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8124  Z= 0.133
  Angle     :  0.588   9.683  11124  Z= 0.268
  Chirality :  0.034   0.181   1422
  Planarity :  0.002   0.021   1206
  Dihedral  :  4.562  54.326   1013
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 23.79 %
    Favored  : 71.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.54 (0.27), residues: 954
  helix:  2.71 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.58 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  73 
 TYR   0.010   0.001   TYR B  41 
 PHE   0.009   0.001   PHE E 112 
 TRP   0.008   0.001   TRP F 164 
 HIS   0.001   0.000   HIS C 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8124)
  covalent geometry    : angle       0.58757 (11124)
  hydrogen bonds       : bond        0.03349 (  683)
  hydrogen bonds       : angle       3.18147 ( 2037)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 158
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: C  113 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8290 (mp)
REVERT: C  158 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7395 (mm)
REVERT: E   94 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7282 (tt)
REVERT: F  113 ILE cc_start: 0.8032 (tp) cc_final: 0.7578 (pt)
REVERT: F  155 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8577 (mt)
REVERT: A   94 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7243 (tt)
REVERT: B  113 ILE cc_start: 0.8062 (tp) cc_final: 0.7634 (pt)
REVERT: B  155 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8586 (mt)
REVERT: D   44 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7491 (mpp)
REVERT: D  113 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8300 (mp)
REVERT: D  158 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7404 (mm)
  outliers start: 36
  outliers final: 26
  residues processed: 175
  average time/residue: 0.0621
  time to fit residues: 16.4811
Evaluate side-chains
  192 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 157
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue   94 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  184 MET
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain F residue  181 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   98 TRP
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  143 PHE
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain D residue  158 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9980
   chunk 94 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 69 optimal weight:    0.0270
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
B 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.215388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.177305 restraints weight = 9712.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.180760 restraints weight = 6612.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.182962 restraints weight = 5245.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.183838 restraints weight = 4569.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.183839 restraints weight = 4268.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.4308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8124  Z= 0.122
  Angle     :  0.576   9.496  11124  Z= 0.264
  Chirality :  0.034   0.181   1422
  Planarity :  0.002   0.022   1206
  Dihedral  :  4.535  54.192   1013
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 23.79 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.62 (0.27), residues: 954
  helix:  2.76 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.53 (0.70), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  73 
 TYR   0.010   0.001   TYR B  41 
 PHE   0.008   0.001   PHE D  58 
 TRP   0.020   0.001   TRP A 131 
 HIS   0.001   0.000   HIS C 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8124)
  covalent geometry    : angle       0.57594 (11124)
  hydrogen bonds       : bond        0.03232 (  683)
  hydrogen bonds       : angle       3.14711 ( 2037)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 158
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
REVERT: C  113 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8282 (mp)
REVERT: C  158 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7393 (mm)
REVERT: E   94 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7275 (tt)
REVERT: F  113 ILE cc_start: 0.8008 (tp) cc_final: 0.7544 (pt)
REVERT: F  155 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8554 (mt)
REVERT: A   94 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7191 (tt)
REVERT: B  113 ILE cc_start: 0.8047 (tp) cc_final: 0.7615 (pt)
REVERT: B  155 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8571 (mt)
REVERT: D   44 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7534 (mpp)
REVERT: D  113 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8254 (mp)
REVERT: D  158 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7410 (mm)
  outliers start: 35
  outliers final: 25
  residues processed: 174
  average time/residue: 0.0627
  time to fit residues: 16.6344
Evaluate side-chains
  190 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 156
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain C residue  144 ILE
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue   94 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  184 MET
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain F residue  181 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   98 TRP
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  143 PHE
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain D residue  158 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.213511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.175395 restraints weight = 9738.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.178807 restraints weight = 6599.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.180364 restraints weight = 5221.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.182045 restraints weight = 4629.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.182625 restraints weight = 4252.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.4297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8124  Z= 0.137
  Angle     :  0.599   9.446  11124  Z= 0.273
  Chirality :  0.034   0.179   1422
  Planarity :  0.002   0.021   1206
  Dihedral  :  4.307  53.765   1011
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 23.91 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.56 (0.27), residues: 954
  helix:  2.72 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.55 (0.70), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  74 
 TYR   0.011   0.001   TYR B  41 
 PHE   0.009   0.001   PHE E 112 
 TRP   0.018   0.001   TRP E 131 
 HIS   0.001   0.000   HIS C 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8124)
  covalent geometry    : angle       0.59931 (11124)
  hydrogen bonds       : bond        0.03342 (  683)
  hydrogen bonds       : angle       3.17908 ( 2037)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1638.99 seconds
wall clock time: 28 minutes 50.01 seconds (1730.01 seconds total)