Starting phenix.real_space_refine
on Wed Sep 17 04:29:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jst_61782/09_2025/9jst_61782.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jst_61782/09_2025/9jst_61782.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jst_61782/09_2025/9jst_61782.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jst_61782/09_2025/9jst_61782.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jst_61782/09_2025/9jst_61782.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jst_61782/09_2025/9jst_61782.cif"
  }
  resolution = 1.79
  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=   0.010 sd=   0.099
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: 5
    Type Number    sf(0)   Gaussians
     S       8      5.16       5
     C    1440      2.51       5
     N     368      2.21       5
     O     360      1.98       5
     H    2128      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4304
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 538
          Classifications: {'peptide': 35}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 33}
    Chain: "B"
      Number of atoms: 538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 538
          Classifications: {'peptide': 35}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 33}
    Chain: "C"
      Number of atoms: 538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 538
          Classifications: {'peptide': 35}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 33}
    Chain: "D"
      Number of atoms: 538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 538
          Classifications: {'peptide': 35}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 33}
    Chain: "E"
      Number of atoms: 538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 538
          Classifications: {'peptide': 35}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 33}
    Chain: "F"
      Number of atoms: 538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 538
          Classifications: {'peptide': 35}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 33}
    Chain: "G"
      Number of atoms: 538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 538
          Classifications: {'peptide': 35}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 33}
    Chain: "H"
      Number of atoms: 538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 538
          Classifications: {'peptide': 35}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 33}
  Time building chain proxies: 1.18, per 1000 atoms: 0.27
  Number of scatterers: 4304
  At special positions: 0
  Unit cell: (73.7856, 75.5424, 49.1904, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       8     16.00
     O     360      8.00
     N     368      7.00
     C    1440      6.00
     H    2128      1.00
    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: 0.35
  Conformation dependent library (CDL) restraints added in 105.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  448

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 4 sheets defined
      0.0% alpha, 77.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 164
    Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 179
      removed outlier: 6.866A  pdb=" N   LEU B 170 " --> pdb=" O   GLY A 169 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   SER A 171 " --> pdb=" O   LEU B 170 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   ILE B 172 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   GLY A 173 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   THR B 174 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLY A 175 " --> pdb=" O   THR B 174 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   LEU C 170 " --> pdb=" O   GLY B 169 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   SER B 171 " --> pdb=" O   LEU C 170 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   ILE C 172 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   GLY B 173 " --> pdb=" O   ILE C 172 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLY B 175 " --> pdb=" O   THR C 174 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ARG C 176 " --> pdb=" O   GLY B 175 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   VAL C 167 " --> pdb=" O   SER D 168 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   LEU D 170 " --> pdb=" O   VAL C 167 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   GLY C 169 " --> pdb=" O   LEU D 170 " (cutoff:3.500A)
      removed outlier: 10.637A  pdb=" N   ILE D 172 " --> pdb=" O   GLY C 169 " (cutoff:3.500A)
      removed outlier: 9.210A  pdb=" N   SER C 171 " --> pdb=" O   ILE D 172 " (cutoff:3.500A)
      removed outlier: 10.318A  pdb=" N   THR D 174 " --> pdb=" O   SER C 171 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   GLY C 173 " --> pdb=" O   THR D 174 " (cutoff:3.500A)
      removed outlier: 8.427A  pdb=" N   ARG D 176 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   GLY C 175 " --> pdb=" O   ARG D 176 " (cutoff:3.500A)
      removed outlier: 8.402A  pdb=" N   MET D 178 " --> pdb=" O   GLY C 175 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ALA C 177 " --> pdb=" O   MET D 178 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 149 through 164
      removed outlier: 6.421A  pdb=" N   VAL G 150 " --> pdb=" O   TYR H 151 " (cutoff:3.500A)
      removed outlier: 7.965A  pdb=" N   TRP H 153 " --> pdb=" O   VAL G 150 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   VAL G 152 " --> pdb=" O   TRP H 153 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   THR H 155 " --> pdb=" O   VAL G 152 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   LYS G 154 " --> pdb=" O   THR H 155 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   GLY H 157 " --> pdb=" O   LYS G 154 " (cutoff:3.500A)
      removed outlier: 5.770A  pdb=" N   TRP G 156 " --> pdb=" O   GLY H 157 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   TYR H 159 " --> pdb=" O   TRP G 156 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   GLN G 158 " --> pdb=" O   TYR H 159 " (cutoff:3.500A)
      removed outlier: 8.237A  pdb=" N   GLN H 161 " --> pdb=" O   GLN G 158 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   TRP G 160 " --> pdb=" O   GLN H 161 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   LEU H 163 " --> pdb=" O   TRP G 160 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   VAL G 162 " --> pdb=" O   LEU H 163 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 167 through 179
      removed outlier: 6.402A  pdb=" N   VAL E 167 " --> pdb=" O   SER F 168 " (cutoff:3.500A)
      removed outlier: 7.503A  pdb=" N   LEU F 170 " --> pdb=" O   VAL E 167 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   GLY E 169 " --> pdb=" O   LEU F 170 " (cutoff:3.500A)
      removed outlier: 10.567A  pdb=" N   ILE F 172 " --> pdb=" O   GLY E 169 " (cutoff:3.500A)
      removed outlier: 9.181A  pdb=" N   SER E 171 " --> pdb=" O   ILE F 172 " (cutoff:3.500A)
      removed outlier: 10.477A  pdb=" N   THR F 174 " --> pdb=" O   SER E 171 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   GLY E 173 " --> pdb=" O   THR F 174 " (cutoff:3.500A)
      removed outlier: 8.488A  pdb=" N   ARG F 176 " --> pdb=" O   GLY E 173 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   GLY E 175 " --> pdb=" O   ARG F 176 " (cutoff:3.500A)
      removed outlier: 8.455A  pdb=" N   MET F 178 " --> pdb=" O   GLY E 175 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ALA E 177 " --> pdb=" O   MET F 178 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   VAL F 167 " --> pdb=" O   SER G 168 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   LEU G 170 " --> pdb=" O   VAL F 167 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   GLY F 169 " --> pdb=" O   LEU G 170 " (cutoff:3.500A)
      removed outlier: 10.626A  pdb=" N   ILE G 172 " --> pdb=" O   GLY F 169 " (cutoff:3.500A)
      removed outlier: 9.246A  pdb=" N   SER F 171 " --> pdb=" O   ILE G 172 " (cutoff:3.500A)
      removed outlier: 10.434A  pdb=" N   THR G 174 " --> pdb=" O   SER F 171 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   GLY F 173 " --> pdb=" O   THR G 174 " (cutoff:3.500A)
      removed outlier: 8.579A  pdb=" N   ARG G 176 " --> pdb=" O   GLY F 173 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   GLY F 175 " --> pdb=" O   ARG G 176 " (cutoff:3.500A)
      removed outlier: 8.459A  pdb=" N   MET G 178 " --> pdb=" O   GLY F 175 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ALA F 177 " --> pdb=" O   MET G 178 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   LEU H 170 " --> pdb=" O   GLY G 169 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   SER G 171 " --> pdb=" O   LEU H 170 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   ILE H 172 " --> pdb=" O   SER G 171 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   GLY G 173 " --> pdb=" O   ILE H 172 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   THR H 174 " --> pdb=" O   GLY G 173 " (cutoff:3.500A)

    94 hydrogen bonds defined for protein.
    282 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: 0.96

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        0.94 -     1.12: 2128
        1.12 -     1.29: 296
        1.29 -     1.47: 967
        1.47 -     1.64: 977
        1.64 -     1.81: 16
  Bond restraints: 4384
  Sorted by residual:
  bond pdb=" CD1 TRP C 153 "
       pdb=" HD1 TRP C 153 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" CD1 TRP B 156 "
       pdb=" HD1 TRP B 156 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" CD1 TYR D 151 "
       pdb=" HD1 TYR D 151 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" CZ2 TRP C 156 "
       pdb=" HZ2 TRP C 156 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" CE1 TYR E 159 "
       pdb=" HE1 TYR E 159 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.65e+01
  ... (remaining 4379 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 6045
        1.90 -     3.81: 1311
        3.81 -     5.71: 349
        5.71 -     7.61: 122
        7.61 -     9.52: 13
  Bond angle restraints: 7840
  Sorted by residual:
  angle pdb=" N   GLY G 164 "
        pdb=" CA  GLY G 164 "
        pdb=" C   GLY G 164 "
      ideal   model   delta    sigma   weight residual
     110.80  120.32   -9.52 1.41e+00 5.03e-01 4.56e+01
  angle pdb=" N   GLY F 164 "
        pdb=" CA  GLY F 164 "
        pdb=" C   GLY F 164 "
      ideal   model   delta    sigma   weight residual
     110.80  120.13   -9.33 1.41e+00 5.03e-01 4.38e+01
  angle pdb=" N   GLY B 164 "
        pdb=" CA  GLY B 164 "
        pdb=" C   GLY B 164 "
      ideal   model   delta    sigma   weight residual
     110.80  120.00   -9.20 1.41e+00 5.03e-01 4.26e+01
  angle pdb=" N   GLY C 164 "
        pdb=" CA  GLY C 164 "
        pdb=" C   GLY C 164 "
      ideal   model   delta    sigma   weight residual
     110.80  119.69   -8.89 1.41e+00 5.03e-01 3.97e+01
  angle pdb=" N   GLY E 164 "
        pdb=" CA  GLY E 164 "
        pdb=" C   GLY E 164 "
      ideal   model   delta    sigma   weight residual
     110.74  117.75   -7.01 1.37e+00 5.33e-01 2.62e+01
  ... (remaining 7835 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.08: 1750
       13.08 -    26.16: 124
       26.16 -    39.23: 23
       39.23 -    52.31: 55
       52.31 -    65.39: 88
  Dihedral angle restraints: 2040
    sinusoidal: 1032
      harmonic: 1008
  Sorted by residual:
  dihedral pdb=" CA  LEU B 163 "
           pdb=" C   LEU B 163 "
           pdb=" N   GLY B 164 "
           pdb=" CA  GLY B 164 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.39  -26.61     0      5.00e+00 4.00e-02 2.83e+01
  dihedral pdb=" CA  LEU F 163 "
           pdb=" C   LEU F 163 "
           pdb=" N   GLY F 164 "
           pdb=" CA  GLY F 164 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.46  -25.54     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  TRP C 160 "
           pdb=" C   TRP C 160 "
           pdb=" N   GLN C 161 "
           pdb=" CA  GLN C 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.25   23.75     0      5.00e+00 4.00e-02 2.26e+01
  ... (remaining 2037 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.061: 173
       0.061 -    0.121: 118
       0.121 -    0.180: 13
       0.180 -    0.240: 0
       0.240 -    0.299: 8
  Chirality restraints: 312
  Sorted by residual:
  chirality pdb=" CA  SER G 148 "
            pdb=" N   SER G 148 "
            pdb=" C   SER G 148 "
            pdb=" CB  SER G 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.27    0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" CA  SER C 148 "
            pdb=" N   SER C 148 "
            pdb=" C   SER C 148 "
            pdb=" CB  SER C 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.28    0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" CA  SER H 148 "
            pdb=" N   SER H 148 "
            pdb=" C   SER H 148 "
            pdb=" CB  SER H 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.28    0.29 2.00e-01 2.50e+01 2.09e+00
  ... (remaining 309 not shown)

  Planarity restraints: 624
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP G 160 "    0.048 2.00e-02 2.50e+03   3.95e-02 6.25e+01
        pdb=" CG  TRP G 160 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 TRP G 160 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP G 160 "    0.026 2.00e-02 2.50e+03
        pdb=" NE1 TRP G 160 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 TRP G 160 "    0.030 2.00e-02 2.50e+03
        pdb=" CE3 TRP G 160 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ2 TRP G 160 "    0.042 2.00e-02 2.50e+03
        pdb=" CZ3 TRP G 160 "   -0.025 2.00e-02 2.50e+03
        pdb=" CH2 TRP G 160 "    0.007 2.00e-02 2.50e+03
        pdb=" HD1 TRP G 160 "   -0.026 2.00e-02 2.50e+03
        pdb=" HE1 TRP G 160 "   -0.100 2.00e-02 2.50e+03
        pdb=" HE3 TRP G 160 "   -0.034 2.00e-02 2.50e+03
        pdb=" HZ2 TRP G 160 "    0.056 2.00e-02 2.50e+03
        pdb=" HZ3 TRP G 160 "   -0.044 2.00e-02 2.50e+03
        pdb=" HH2 TRP G 160 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 153 "    0.089 2.00e-02 2.50e+03   3.86e-02 5.96e+01
        pdb=" CG  TRP D 153 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 153 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 153 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 153 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 153 "    0.010 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 153 "   -0.032 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 153 "    0.033 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 153 "   -0.027 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 153 "    0.021 2.00e-02 2.50e+03
        pdb=" HD1 TRP D 153 "   -0.022 2.00e-02 2.50e+03
        pdb=" HE1 TRP D 153 "   -0.070 2.00e-02 2.50e+03
        pdb=" HE3 TRP D 153 "   -0.032 2.00e-02 2.50e+03
        pdb=" HZ2 TRP D 153 "    0.048 2.00e-02 2.50e+03
        pdb=" HZ3 TRP D 153 "   -0.040 2.00e-02 2.50e+03
        pdb=" HH2 TRP D 153 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 160 "   -0.032 2.00e-02 2.50e+03   3.58e-02 5.12e+01
        pdb=" CG  TRP B 160 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 160 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 160 "   -0.020 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 160 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 160 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 160 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 160 "   -0.032 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 160 "    0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 160 "   -0.002 2.00e-02 2.50e+03
        pdb=" HD1 TRP B 160 "    0.006 2.00e-02 2.50e+03
        pdb=" HE1 TRP B 160 "    0.102 2.00e-02 2.50e+03
        pdb=" HE3 TRP B 160 "    0.031 2.00e-02 2.50e+03
        pdb=" HZ2 TRP B 160 "   -0.055 2.00e-02 2.50e+03
        pdb=" HZ3 TRP B 160 "    0.034 2.00e-02 2.50e+03
        pdb=" HH2 TRP B 160 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 621 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.36: 751
        2.36 -     2.92: 8880
        2.92 -     3.48: 11156
        3.48 -     4.04: 15822
        4.04 -     4.60: 20968
  Nonbonded interactions: 57577
  Sorted by model distance:
  nonbonded pdb=" O   VAL G 162 "
            pdb=" H   LEU H 163 "
     model   vdw
     1.795 2.450
  nonbonded pdb="HE21 GLN F 161 "
            pdb=" OE1 GLN G 161 "
     model   vdw
     1.814 2.450
  nonbonded pdb=" H   VAL G 162 "
            pdb=" O   GLN H 161 "
     model   vdw
     1.816 2.450
  nonbonded pdb="HE21 GLN B 161 "
            pdb=" OE1 GLN C 161 "
     model   vdw
     1.817 2.450
  nonbonded pdb="HE21 GLN A 161 "
            pdb=" OE1 GLN B 161 "
     model   vdw
     1.817 2.450
  ... (remaining 57572 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.040
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.610
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8946
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      :  0.012   0.037   2256  Z= 0.733
  Angle     :  1.743   9.519   3072  Z= 1.159
  Chirality :  0.080   0.299    312
  Planarity :  0.010   0.038    360
  Dihedral  : 10.675  48.282    712
  Min Nonbonded Distance : 2.662

Molprobity Statistics.
  All-atom Clashscore : 1.17
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  4.92 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.44), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.32 (0.33), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 176 
 TYR   0.066   0.013   TYR E 151 
 PHE   0.014   0.004   PHE G 149 
 TRP   0.055   0.013   TRP D 153 
 HIS   0.007   0.002   HIS G 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.01247 ( 2256)
  covalent geometry    : angle       1.74306 ( 3072)
  hydrogen bonds       : bond        0.14320 (   94)
  hydrogen bonds       : angle       8.05502 (  282)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 1.5339
  time to fit residues: 66.9296
Evaluate side-chains
  43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 18 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    5.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.155642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.112108 restraints weight = 3903.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 1.39
r_work: 0.3306 rms_B_bonded: 1.24 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 1.89 restraints_weight: 0.2500
r_work: 0.3092 rms_B_bonded: 4.22 restraints_weight: 0.1250
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9314
moved from start:          0.2855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2256  Z= 0.136
  Angle     :  0.613   3.960   3072  Z= 0.335
  Chirality :  0.051   0.124    312
  Planarity :  0.005   0.041    360
  Dihedral  :  7.199  23.916    296
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 0.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  6.94 %
    Favored  : 92.59 %
  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: -1.88 (0.43), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.42 (0.33), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 176 
 TYR   0.007   0.001   TYR B 159 
 PHE   0.003   0.001   PHE A 149 
 TRP   0.011   0.002   TRP B 153 
 HIS   0.002   0.001   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 2256)
  covalent geometry    : angle       0.61321 ( 3072)
  hydrogen bonds       : bond        0.03969 (   94)
  hydrogen bonds       : angle       6.20917 (  282)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 41
  average time/residue: 1.6543
  time to fit residues: 68.7387
Evaluate side-chains
  41 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  148 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 20 optimal weight:   30.0000
   chunk 10 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 1 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 17 optimal weight:   10.0000
   chunk 8 optimal weight:   20.0000
   chunk 5 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    5.7588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.155636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.112460 restraints weight = 3859.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.37
r_work: 0.3305 rms_B_bonded: 1.24 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 1.88 restraints_weight: 0.2500
r_work: 0.3085 rms_B_bonded: 4.19 restraints_weight: 0.1250
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9314
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2256  Z= 0.123
  Angle     :  0.583   4.184   3072  Z= 0.314
  Chirality :  0.051   0.129    312
  Planarity :  0.004   0.037    360
  Dihedral  :  7.127  24.720    296
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 0.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  6.02 %
    Favored  : 92.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.79 (0.44), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.36 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 176 
 TYR   0.006   0.001   TYR H 159 
 PHE   0.005   0.001   PHE C 149 
 TRP   0.011   0.002   TRP B 153 
 HIS   0.001   0.000   HIS E 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 2256)
  covalent geometry    : angle       0.58254 ( 3072)
  hydrogen bonds       : bond        0.03631 (   94)
  hydrogen bonds       : angle       5.70232 (  282)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 4
  residues processed: 41
  average time/residue: 1.8943
  time to fit residues: 78.6987
Evaluate side-chains
  44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain D residue  148 SER
Chi-restraints excluded: chain F residue  148 SER
Chi-restraints excluded: chain H residue  148 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 6 optimal weight:   20.0000
   chunk 8 optimal weight:    0.9990
   chunk 7 optimal weight:    9.9990
   chunk 3 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   overall best weight:    3.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.157338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.114595 restraints weight = 3814.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.36
r_work: 0.3338 rms_B_bonded: 1.24 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 1.89 restraints_weight: 0.2500
r_work: 0.3119 rms_B_bonded: 4.22 restraints_weight: 0.1250
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9290
moved from start:          0.3219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2256  Z= 0.098
  Angle     :  0.539   4.256   3072  Z= 0.287
  Chirality :  0.050   0.126    312
  Planarity :  0.003   0.033    360
  Dihedral  :  6.701  22.450    296
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 0.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  6.02 %
    Favored  : 92.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.69 (0.46), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.28 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 176 
 TYR   0.004   0.001   TYR B 159 
 PHE   0.003   0.001   PHE C 149 
 TRP   0.009   0.001   TRP B 153 
 HIS   0.001   0.000   HIS G 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 2256)
  covalent geometry    : angle       0.53851 ( 3072)
  hydrogen bonds       : bond        0.02867 (   94)
  hydrogen bonds       : angle       5.29297 (  282)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
REVERT: F  154 LYS cc_start: 0.9233 (mttm) cc_final: 0.9021 (mttt)
  outliers start: 4
  outliers final: 4
  residues processed: 38
  average time/residue: 1.9062
  time to fit residues: 73.3454
Evaluate side-chains
  40 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain D residue  148 SER
Chi-restraints excluded: chain F residue  148 SER
Chi-restraints excluded: chain H residue  148 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 18 optimal weight:    9.9990
   chunk 8 optimal weight:   30.0000
   chunk 6 optimal weight:   20.0000
   chunk 23 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 9 optimal weight:    7.9990
   chunk 2 optimal weight:   30.0000
   chunk 13 optimal weight:    9.9990
   chunk 17 optimal weight:   30.0000
   overall best weight:    6.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.154721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.111438 restraints weight = 3838.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 1.37
r_work: 0.3287 rms_B_bonded: 1.25 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 1.90 restraints_weight: 0.2500
r_work: 0.3066 rms_B_bonded: 4.21 restraints_weight: 0.1250
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9316
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2256  Z= 0.139
  Angle     :  0.601   4.291   3072  Z= 0.322
  Chirality :  0.051   0.127    312
  Planarity :  0.004   0.034    360
  Dihedral  :  7.165  26.200    296
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 0.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  5.09 %
    Favored  : 93.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.45), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.32 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H 176 
 TYR   0.005   0.001   TYR H 159 
 PHE   0.007   0.001   PHE C 149 
 TRP   0.010   0.002   TRP B 153 
 HIS   0.001   0.000   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 2256)
  covalent geometry    : angle       0.60118 ( 3072)
  hydrogen bonds       : bond        0.03835 (   94)
  hydrogen bonds       : angle       5.60700 (  282)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.147 
Fit side-chains
REVERT: F  154 LYS cc_start: 0.9243 (mttm) cc_final: 0.9023 (mttt)
  outliers start: 4
  outliers final: 4
  residues processed: 38
  average time/residue: 2.0211
  time to fit residues: 77.8034
Evaluate side-chains
  40 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain D residue  148 SER
Chi-restraints excluded: chain F residue  148 SER
Chi-restraints excluded: chain H residue  148 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 17 optimal weight:   30.0000
   chunk 19 optimal weight:    9.9990
   chunk 18 optimal weight:    9.9990
   chunk 1 optimal weight:    9.9990
   chunk 8 optimal weight:   20.0000
   chunk 15 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 5 optimal weight:   20.0000
   chunk 22 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   overall best weight:    6.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.155067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.111979 restraints weight = 3930.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.38
r_work: 0.3306 rms_B_bonded: 1.25 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 1.92 restraints_weight: 0.2500
r_work: 0.3086 rms_B_bonded: 4.25 restraints_weight: 0.1250
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9313
moved from start:          0.3319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2256  Z= 0.127
  Angle     :  0.598   4.943   3072  Z= 0.314
  Chirality :  0.051   0.127    312
  Planarity :  0.004   0.035    360
  Dihedral  :  7.041  26.023    296
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 0.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  6.48 %
    Favored  : 91.67 %
  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: -1.76 (0.45), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.33 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 176 
 TYR   0.005   0.001   TYR H 159 
 PHE   0.006   0.001   PHE C 149 
 TRP   0.010   0.002   TRP B 153 
 HIS   0.001   0.000   HIS G 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 2256)
  covalent geometry    : angle       0.59759 ( 3072)
  hydrogen bonds       : bond        0.03504 (   94)
  hydrogen bonds       : angle       5.50260 (  282)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.134 
Fit side-chains
REVERT: F  154 LYS cc_start: 0.9232 (mttm) cc_final: 0.9007 (mttt)
  outliers start: 4
  outliers final: 4
  residues processed: 37
  average time/residue: 2.0314
  time to fit residues: 76.0714
Evaluate side-chains
  39 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain D residue  148 SER
Chi-restraints excluded: chain F residue  148 SER
Chi-restraints excluded: chain H residue  148 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 15 optimal weight:   20.0000
   chunk 20 optimal weight:   30.0000
   chunk 16 optimal weight:    9.9990
   chunk 3 optimal weight:   20.0000
   chunk 0 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 5 optimal weight:   30.0000
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    3.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.157451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.114342 restraints weight = 3942.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 1.39
r_work: 0.3332 rms_B_bonded: 1.27 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 1.94 restraints_weight: 0.2500
r_work: 0.3114 rms_B_bonded: 4.33 restraints_weight: 0.1250
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9286
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2256  Z= 0.097
  Angle     :  0.560   4.836   3072  Z= 0.292
  Chirality :  0.051   0.126    312
  Planarity :  0.003   0.030    360
  Dihedral  :  6.628  22.546    296
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 0.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  6.02 %
    Favored  : 92.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.69 (0.46), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.28 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 176 
 TYR   0.004   0.001   TYR B 159 
 PHE   0.004   0.001   PHE C 149 
 TRP   0.009   0.001   TRP E 153 
 HIS   0.001   0.000   HIS G 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 2256)
  covalent geometry    : angle       0.56037 ( 3072)
  hydrogen bonds       : bond        0.02780 (   94)
  hydrogen bonds       : angle       5.19711 (  282)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.161 
Fit side-chains
REVERT: F  154 LYS cc_start: 0.9222 (mttm) cc_final: 0.8998 (mttt)
  outliers start: 4
  outliers final: 4
  residues processed: 37
  average time/residue: 2.0553
  time to fit residues: 76.9812
Evaluate side-chains
  38 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain D residue  148 SER
Chi-restraints excluded: chain F residue  148 SER
Chi-restraints excluded: chain H residue  148 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 2 optimal weight:   20.0000
   chunk 8 optimal weight:   30.0000
   chunk 20 optimal weight:   30.0000
   chunk 18 optimal weight:    3.9990
   chunk 14 optimal weight:   30.0000
   chunk 7 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    5.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.155202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.111983 restraints weight = 3879.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 1.38
r_work: 0.3309 rms_B_bonded: 1.24 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 1.90 restraints_weight: 0.2500
r_work: 0.3093 rms_B_bonded: 4.22 restraints_weight: 0.1250
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9310
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2256  Z= 0.125
  Angle     :  0.600   5.562   3072  Z= 0.313
  Chirality :  0.051   0.127    312
  Planarity :  0.004   0.033    360
  Dihedral  :  6.968  25.582    296
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 0.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  7.41 %
    Favored  : 90.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.72 (0.46), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.30 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG G 176 
 TYR   0.005   0.001   TYR H 159 
 PHE   0.006   0.001   PHE C 149 
 TRP   0.010   0.002   TRP B 153 
 HIS   0.001   0.000   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 2256)
  covalent geometry    : angle       0.59985 ( 3072)
  hydrogen bonds       : bond        0.03501 (   94)
  hydrogen bonds       : angle       5.44785 (  282)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.149 
Fit side-chains
REVERT: F  154 LYS cc_start: 0.9224 (mttm) cc_final: 0.9001 (mttt)
  outliers start: 4
  outliers final: 4
  residues processed: 37
  average time/residue: 2.0146
  time to fit residues: 75.4594
Evaluate side-chains
  38 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain D residue  148 SER
Chi-restraints excluded: chain F residue  148 SER
Chi-restraints excluded: chain H residue  148 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 15 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 2 optimal weight:   20.0000
   chunk 17 optimal weight:    9.9990
   overall best weight:    6.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.155326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.112299 restraints weight = 3879.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 1.37
r_work: 0.3309 rms_B_bonded: 1.24 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 1.89 restraints_weight: 0.2500
r_work: 0.3093 rms_B_bonded: 4.20 restraints_weight: 0.1250
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9307
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2256  Z= 0.128
  Angle     :  0.604   5.564   3072  Z= 0.315
  Chirality :  0.051   0.127    312
  Planarity :  0.004   0.034    360
  Dihedral  :  6.984  26.008    296
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 0.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  7.41 %
    Favored  : 90.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.76 (0.46), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.33 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H 176 
 TYR   0.004   0.001   TYR B 159 
 PHE   0.006   0.001   PHE C 149 
 TRP   0.010   0.002   TRP B 153 
 HIS   0.001   0.000   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 2256)
  covalent geometry    : angle       0.60422 ( 3072)
  hydrogen bonds       : bond        0.03503 (   94)
  hydrogen bonds       : angle       5.45854 (  282)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.129 
Fit side-chains
REVERT: F  154 LYS cc_start: 0.9219 (mttm) cc_final: 0.8996 (mttt)
  outliers start: 4
  outliers final: 4
  residues processed: 37
  average time/residue: 2.1181
  time to fit residues: 79.3013
Evaluate side-chains
  38 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain D residue  148 SER
Chi-restraints excluded: chain F residue  148 SER
Chi-restraints excluded: chain H residue  148 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 3 optimal weight:   20.0000
   chunk 6 optimal weight:    2.9990
   chunk 20 optimal weight:   30.0000
   chunk 21 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 1 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 12 optimal weight:    0.3980
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    2.4788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.158831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.116056 restraints weight = 3864.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 1.38
r_work: 0.3346 rms_B_bonded: 1.27 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 1.94 restraints_weight: 0.2500
r_work: 0.3128 rms_B_bonded: 4.32 restraints_weight: 0.1250
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9271
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   2256  Z= 0.089
  Angle     :  0.554   5.194   3072  Z= 0.285
  Chirality :  0.051   0.126    312
  Planarity :  0.003   0.028    360
  Dihedral  :  6.413  21.131    296
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 0.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  6.94 %
    Favored  : 91.20 %
  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: -1.67 (0.47), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.26 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG H 176 
 TYR   0.004   0.001   TYR F 159 
 PHE   0.004   0.001   PHE C 149 
 TRP   0.010   0.001   TRP E 153 
 HIS   0.000   0.000   HIS D 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 2256)
  covalent geometry    : angle       0.55425 ( 3072)
  hydrogen bonds       : bond        0.02509 (   94)
  hydrogen bonds       : angle       4.99526 (  282)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.162 
Fit side-chains
REVERT: F  154 LYS cc_start: 0.9214 (mttm) cc_final: 0.8991 (mttt)
  outliers start: 4
  outliers final: 4
  residues processed: 37
  average time/residue: 2.0668
  time to fit residues: 77.4387
Evaluate side-chains
  37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain D residue  148 SER
Chi-restraints excluded: chain F residue  148 SER
Chi-restraints excluded: chain H residue  148 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 22 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 14 optimal weight:   20.0000
   chunk 1 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 21 optimal weight:    8.9990
   overall best weight:    7.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.154734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.111492 restraints weight = 3882.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 1.37
r_work: 0.3301 rms_B_bonded: 1.24 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 1.89 restraints_weight: 0.2500
r_work: 0.3085 rms_B_bonded: 4.19 restraints_weight: 0.1250
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9310
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2256  Z= 0.144
  Angle     :  0.617   5.392   3072  Z= 0.323
  Chirality :  0.051   0.127    312
  Planarity :  0.004   0.033    360
  Dihedral  :  7.047  26.101    296
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  7.41 %
    Favored  : 90.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.74 (0.47), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.32 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 176 
 TYR   0.005   0.001   TYR H 159 
 PHE   0.007   0.001   PHE C 149 
 TRP   0.009   0.002   TRP B 153 
 HIS   0.001   0.000   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 2256)
  covalent geometry    : angle       0.61741 ( 3072)
  hydrogen bonds       : bond        0.03793 (   94)
  hydrogen bonds       : angle       5.50731 (  282)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3493.07 seconds
wall clock time: 59 minutes 49.54 seconds (3589.54 seconds total)