Starting phenix.real_space_refine
on Tue Feb 11 16:30:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gmt_34153/02_2025/8gmt_34153.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gmt_34153/02_2025/8gmt_34153.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gmt_34153/02_2025/8gmt_34153.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gmt_34153/02_2025/8gmt_34153.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gmt_34153/02_2025/8gmt_34153.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gmt_34153/02_2025/8gmt_34153.cif"
  }
  resolution = 3.31
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 6
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     Mg      2      5.21       5
     S      29      5.16       5
     C    3854      2.51       5
     N    1045      2.21       5
     O    1230      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6172
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 250
          Classifications: {'peptide': 32}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 28}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 722
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "S"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 120
          Classifications: {'DNA': 6}
          Link IDs: {'rna3p': 5}
    Chain: "F"
      Number of atoms: 2508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2508
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 9, 'TRANS': 323}
    Chain: "G"
      Number of atoms: 2508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2508
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 9, 'TRANS': 323}
    Chain: "F"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "G"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.10, per 1000 atoms: 0.66
  Number of scatterers: 6172
  At special positions: 0
  Unit cell: (99.96, 95.2, 105.91, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      29     16.00
     P      12     15.00
     Mg      2     11.99
     O    1230      8.00
     N    1045      7.00
     C    3854      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: 1.48
  Conformation dependent library (CDL) restraints added in 908.8 milliseconds
  

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1440

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      42.8% alpha, 27.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'B' and resid 39 through 45
    Processing helix  chain 'A' and resid 40 through 45
    Processing helix  chain 'A' and resid 47 through 49
      No H-bonds generated for 'chain 'A' and resid 47 through 49'
    Processing helix  chain 'A' and resid 61 through 65
    Processing helix  chain 'F' and resid 2 through 22
    Processing helix  chain 'F' and resid 30 through 36
      removed outlier: 5.791A  pdb=" N   ARG F  33 " --> pdb=" O   GLY F  30 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   SER F  34 " --> pdb=" O   GLU F  31 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 44 through 52
    Processing helix  chain 'F' and resid 71 through 86
      removed outlier: 3.631A  pdb=" N   GLU F  86 " --> pdb=" O   ALA F  82 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 100 through 107
    Processing helix  chain 'F' and resid 121 through 136
      removed outlier: 3.598A  pdb=" N   GLY F 136 " --> pdb=" O   LEU F 132 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 145 through 149
    Processing helix  chain 'F' and resid 151 through 157
    Processing helix  chain 'F' and resid 165 through 186
      removed outlier: 4.915A  pdb=" N   GLY F 180 " --> pdb=" O   ARG F 176 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   ASN F 181 " --> pdb=" O   LYS F 177 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 213 through 219
    Processing helix  chain 'F' and resid 269 through 281
    Processing helix  chain 'F' and resid 301 through 312
    Processing helix  chain 'F' and resid 313 through 328
    Processing helix  chain 'G' and resid 2 through 22
    Processing helix  chain 'G' and resid 28 through 36
      removed outlier: 3.520A  pdb=" N   ASP G  32 " --> pdb=" O   LEU G  29 " (cutoff:3.500A)
      removed outlier: 5.885A  pdb=" N   ARG G  33 " --> pdb=" O   GLY G  30 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   SER G  34 " --> pdb=" O   GLU G  31 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 44 through 51
    Processing helix  chain 'G' and resid 71 through 86
      removed outlier: 3.580A  pdb=" N   GLU G  86 " --> pdb=" O   ALA G  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 100 through 107
    Processing helix  chain 'G' and resid 121 through 136
      removed outlier: 3.530A  pdb=" N   GLY G 136 " --> pdb=" O   LEU G 132 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 145 through 149
    Processing helix  chain 'G' and resid 151 through 157
    Processing helix  chain 'G' and resid 165 through 186
      removed outlier: 4.775A  pdb=" N   GLY G 180 " --> pdb=" O   ARG G 176 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   ASN G 181 " --> pdb=" O   LYS G 177 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 213 through 219
    Processing helix  chain 'G' and resid 269 through 281
    Processing helix  chain 'G' and resid 301 through 312
    Processing helix  chain 'G' and resid 312 through 328
      removed outlier: 3.535A  pdb=" N   LEU G 328 " --> pdb=" O   ARG G 324 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 15 through 18
    Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 23
      removed outlier: 6.082A  pdb=" N   VAL B  22 " --> pdb=" O   SER A  57 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   HIS A 133 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ASP A  75 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
      removed outlier: 5.724A  pdb=" N   VAL A 131 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   ILE A  87 " --> pdb=" O   PHE A 128 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   VAL A 130 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   ILE A  85 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 26 through 28
      removed outlier: 6.438A  pdb=" N   ILE G 141 " --> pdb=" O   ILE G 190 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   ILE G 192 " --> pdb=" O   ILE G 141 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   VAL G 143 " --> pdb=" O   ILE G 192 " (cutoff:3.500A)
      removed outlier: 8.354A  pdb=" N   GLN G 194 " --> pdb=" O   VAL G 143 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 26 through 28
      removed outlier: 6.438A  pdb=" N   ILE G 141 " --> pdb=" O   ILE G 190 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   ILE G 192 " --> pdb=" O   ILE G 141 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   VAL G 143 " --> pdb=" O   ILE G 192 " (cutoff:3.500A)
      removed outlier: 8.354A  pdb=" N   GLN G 194 " --> pdb=" O   VAL G 143 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   VAL G  62 " --> pdb=" O   PHE G 191 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   ASN G 193 " --> pdb=" O   VAL G  62 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   ILE G  64 " --> pdb=" O   ASN G 193 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   ILE G 195 " --> pdb=" O   ILE G  64 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   GLY G  66 " --> pdb=" O   ILE G 195 " (cutoff:3.500A)
      removed outlier: 9.550A  pdb=" N   MET G 197 " --> pdb=" O   GLY G  66 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ILE G  61 " --> pdb=" O   VAL G 221 " (cutoff:3.500A)
      removed outlier: 8.311A  pdb=" N   LEU G 223 " --> pdb=" O   ILE G  61 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   GLU G  63 " --> pdb=" O   LEU G 223 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   ILE G 225 " --> pdb=" O   GLU G  63 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   TYR G  65 " --> pdb=" O   ILE G 225 " (cutoff:3.500A)
      removed outlier: 8.398A  pdb=" N   ARG G 227 " --> pdb=" O   TYR G  65 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ARG G 222 " --> pdb=" O   VAL G 247 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   GLU G 241 " --> pdb=" O   ILE G 228 " (cutoff:3.500A)
      removed outlier: 4.897A  pdb=" N   ALA G 230 " --> pdb=" O   GLY G 239 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   GLY G 239 " --> pdb=" O   ALA G 230 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   LYS G 232 " --> pdb=" O   VAL G 237 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   VAL G 237 " --> pdb=" O   LYS G 232 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 39 through 40
    Processing sheet with id=AA6, first strand: chain 'F' and resid 115 through 117
    Processing sheet with id=AA7, first strand: chain 'F' and resid 115 through 117
      removed outlier: 6.428A  pdb=" N   VAL F  62 " --> pdb=" O   PHE F 191 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   ASN F 193 " --> pdb=" O   VAL F  62 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ILE F  64 " --> pdb=" O   ASN F 193 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   ILE F 195 " --> pdb=" O   ILE F  64 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   GLY F  66 " --> pdb=" O   ILE F 195 " (cutoff:3.500A)
      removed outlier: 9.929A  pdb=" N   MET F 197 " --> pdb=" O   GLY F  66 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   ILE F  61 " --> pdb=" O   VAL F 221 " (cutoff:3.500A)
      removed outlier: 8.392A  pdb=" N   LEU F 223 " --> pdb=" O   ILE F  61 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   GLU F  63 " --> pdb=" O   LEU F 223 " (cutoff:3.500A)
      removed outlier: 7.405A  pdb=" N   ILE F 225 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   TYR F  65 " --> pdb=" O   ILE F 225 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   ARG F 227 " --> pdb=" O   TYR F  65 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   VAL F 221 " --> pdb=" O   ASN F 249 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ASN F 249 " --> pdb=" O   VAL F 221 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   LEU F 223 " --> pdb=" O   VAL F 247 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   VAL F 247 " --> pdb=" O   LEU F 223 " (cutoff:3.500A)
      removed outlier: 5.265A  pdb=" N   ILE F 225 " --> pdb=" O   LYS F 245 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   LYS F 245 " --> pdb=" O   ILE F 225 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   ARG F 227 " --> pdb=" O   ARG F 243 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   ARG F 243 " --> pdb=" O   ARG F 227 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   GLU F 233 " --> pdb=" O   VAL F 237 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   VAL F 237 " --> pdb=" O   GLU F 233 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 285 through 287
      removed outlier: 7.096A  pdb=" N   TYR F 291 " --> pdb=" O   ILE F 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 39 through 40
    Processing sheet with id=AB1, first strand: chain 'G' and resid 285 through 287
      removed outlier: 6.994A  pdb=" N   TYR G 291 " --> pdb=" O   ILE G 298 " (cutoff:3.500A)

    331 hydrogen bonds defined for protein.
    900 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: 2.14

  Time building geometry restraints manager: 1.75 seconds

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

  Histogram of bond lengths:
        1.22 -     1.36: 2059
        1.36 -     1.51: 1517
        1.51 -     1.65: 2635
        1.65 -     1.80: 32
        1.80 -     1.95: 17
  Bond restraints: 6260
  Sorted by residual:
  bond pdb=" CA  SER G 145 "
       pdb=" CB  SER G 145 "
    ideal  model  delta    sigma   weight residual
    1.532  1.498  0.033 1.36e-02 5.41e+03 5.98e+00
  bond pdb=" N   ASP G  94 "
       pdb=" CA  ASP G  94 "
    ideal  model  delta    sigma   weight residual
    1.462  1.490 -0.028 1.26e-02 6.30e+03 4.97e+00
  bond pdb=" N   SER G 145 "
       pdb=" CA  SER G 145 "
    ideal  model  delta    sigma   weight residual
    1.461  1.487 -0.027 1.38e-02 5.25e+03 3.73e+00
  bond pdb=" CG  LEU F 309 "
       pdb=" CD2 LEU F 309 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.39e+00
  bond pdb=" C   ASP G  94 "
       pdb=" O   ASP G  94 "
    ideal  model  delta    sigma   weight residual
    1.233  1.247 -0.014 1.26e-02 6.30e+03 1.18e+00
  ... (remaining 6255 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 8253
        1.33 -     2.67: 189
        2.67 -     4.00: 28
        4.00 -     5.33: 10
        5.33 -     6.67: 1
  Bond angle restraints: 8481
  Sorted by residual:
  angle pdb=" CA  SER G 145 "
        pdb=" C   SER G 145 "
        pdb=" O   SER G 145 "
      ideal   model   delta    sigma   weight residual
     122.45  118.14    4.31 1.30e+00 5.92e-01 1.10e+01
  angle pdb=" C   ASN F 312 "
        pdb=" CA  ASN F 312 "
        pdb=" CB  ASN F 312 "
      ideal   model   delta    sigma   weight residual
     110.02  114.72   -4.70 1.50e+00 4.44e-01 9.82e+00
  angle pdb=" C   ASP B  32 "
        pdb=" N   TYR B  33 "
        pdb=" CA  TYR B  33 "
      ideal   model   delta    sigma   weight residual
     123.34  118.15    5.19 1.80e+00 3.09e-01 8.33e+00
  angle pdb=" C   TRP F 308 "
        pdb=" CA  TRP F 308 "
        pdb=" CB  TRP F 308 "
      ideal   model   delta    sigma   weight residual
     110.88  106.39    4.49 1.57e+00 4.06e-01 8.17e+00
  angle pdb=" N   ILE A 132 "
        pdb=" CA  ILE A 132 "
        pdb=" C   ILE A 132 "
      ideal   model   delta    sigma   weight residual
     112.96  110.25    2.71 1.00e+00 1.00e+00 7.35e+00
  ... (remaining 8476 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.35: 3542
       29.35 -    58.69: 245
       58.69 -    88.04: 17
       88.04 -   117.39: 0
      117.39 -   146.74: 2
  Dihedral angle restraints: 3806
    sinusoidal: 1557
      harmonic: 2249
  Sorted by residual:
  dihedral pdb=" O1A AGS G 402 "
           pdb=" O3A AGS G 402 "
           pdb=" PA  AGS G 402 "
           pdb=" PB  AGS G 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.73   79.01 -146.74     1      3.00e+01 1.11e-03 1.96e+01
  dihedral pdb=" O1A AGS F 402 "
           pdb=" O3A AGS F 402 "
           pdb=" PA  AGS F 402 "
           pdb=" PB  AGS F 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.73   75.30 -143.03     1      3.00e+01 1.11e-03 1.92e+01
  dihedral pdb=" CA  VAL B  34 "
           pdb=" C   VAL B  34 "
           pdb=" N   GLU B  35 "
           pdb=" CA  GLU B  35 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.68  -18.32     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 3803 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 690
       0.036 -    0.072: 198
       0.072 -    0.108: 75
       0.108 -    0.144: 24
       0.144 -    0.180: 2
  Chirality restraints: 989
  Sorted by residual:
  chirality pdb=" CA  SER G 145 "
            pdb=" N   SER G 145 "
            pdb=" C   SER G 145 "
            pdb=" CB  SER G 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.12e-01
  chirality pdb=" CB  THR G 208 "
            pdb=" CA  THR G 208 "
            pdb=" OG1 THR G 208 "
            pdb=" CG2 THR G 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.41e-01
  chirality pdb=" CA  ILE A  87 "
            pdb=" N   ILE A  87 "
            pdb=" C   ILE A  87 "
            pdb=" CB  ILE A  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.03e-01
  ... (remaining 986 not shown)

  Planarity restraints: 1069
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP F 308 "    0.012 2.00e-02 2.50e+03   2.46e-02 1.51e+01
        pdb=" CG  TRP F 308 "   -0.065 2.00e-02 2.50e+03
        pdb=" CD1 TRP F 308 "    0.034 2.00e-02 2.50e+03
        pdb=" CD2 TRP F 308 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP F 308 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TRP F 308 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP F 308 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ2 TRP F 308 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ3 TRP F 308 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP F 308 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN F 312 "   -0.056 5.00e-02 4.00e+02   8.52e-02 1.16e+01
        pdb=" N   PRO F 313 "    0.147 5.00e-02 4.00e+02
        pdb=" CA  PRO F 313 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO F 313 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN F 312 "   -0.009 2.00e-02 2.50e+03   1.87e-02 3.50e+00
        pdb=" C   ASN F 312 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ASN F 312 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   PRO F 313 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1066 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.58: 53
        2.58 -     3.16: 4740
        3.16 -     3.74: 9527
        3.74 -     4.32: 13337
        4.32 -     4.90: 22512
  Nonbonded interactions: 50169
  Sorted by model distance:
  nonbonded pdb=" OG1 THR G  73 "
            pdb="MG    MG G 401 "
     model   vdw
     1.995 2.170
  nonbonded pdb=" O   CYS B  24 "
            pdb=" OG  SER A  60 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OG  SER F  44 "
            pdb=" OE2 GLU F 273 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   GLN F 300 "
            pdb=" ND2 ASN F 304 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O1B AGS G 402 "
            pdb=" O2G AGS G 402 "
     model   vdw
     2.247 3.040
  ... (remaining 50164 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 'F'
  selection = chain 'G'
}

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:             0.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.370
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
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      :  0.003   0.039   6260  Z= 0.188
  Angle     :  0.519   6.667   8481  Z= 0.308
  Chirality :  0.043   0.180    989
  Planarity :  0.004   0.085   1069
  Dihedral  : 18.125 146.736   2366
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 17.19 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.30), residues: 788
  helix:  1.55 (0.30), residues: 317
  sheet:  1.53 (0.42), residues: 132
  loop : -0.52 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.005   TRP F 308 
 HIS   0.002   0.001   HIS G  97 
 PHE   0.008   0.001   PHE A 128 
 TYR   0.026   0.001   TYR B  33 
 ARG   0.008   0.000   ARG G 134 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.665 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 64
  average time/residue: 0.1865
  time to fit residues: 16.1363
Evaluate side-chains
  61 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  150 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 59 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 61 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    9.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    3.5388

-------------------------------------------------------------------------------
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 = 0.3775 r_free = 0.3775 target = 0.164484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.108968 restraints weight = 6922.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 1.74
r_work: 0.3002 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.1185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047   6260  Z= 0.446
  Angle     :  0.627   5.377   8481  Z= 0.338
  Chirality :  0.050   0.174    989
  Planarity :  0.005   0.067   1069
  Dihedral  : 13.098 147.856    937
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 15.77 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.29), residues: 788
  helix:  1.28 (0.29), residues: 305
  sheet:  0.78 (0.40), residues: 143
  loop : -0.60 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.004   TRP F 308 
 HIS   0.003   0.001   HIS G  97 
 PHE   0.014   0.002   PHE F 217 
 TYR   0.012   0.002   TYR A  52 
 ARG   0.005   0.001   ARG F 169 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 61
  time to evaluate  : 0.654 
Fit side-chains
REVERT: F  203 PHE cc_start: 0.6257 (t80) cc_final: 0.5926 (t80)
REVERT: G  164 MET cc_start: 0.5504 (ptm) cc_final: 0.4837 (ptm)
  outliers start: 22
  outliers final: 16
  residues processed: 75
  average time/residue: 0.1736
  time to fit residues: 17.9492
Evaluate side-chains
  75 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  152 LYS
Chi-restraints excluded: chain F residue  202 MET
Chi-restraints excluded: chain F residue  309 LEU
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  145 SER
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  150 THR
Chi-restraints excluded: chain G residue  172 SER
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  210 THR
Chi-restraints excluded: chain G residue  236 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.167036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.116602 restraints weight = 6919.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 1.92
r_work: 0.3037 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.1242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6260  Z= 0.210
  Angle     :  0.483   4.530   8481  Z= 0.266
  Chirality :  0.045   0.169    989
  Planarity :  0.004   0.055   1069
  Dihedral  : 12.790 143.446    937
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.98 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.30), residues: 788
  helix:  1.26 (0.30), residues: 317
  sheet:  0.78 (0.41), residues: 143
  loop : -0.56 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP F 308 
 HIS   0.002   0.001   HIS G  97 
 PHE   0.009   0.001   PHE F 217 
 TYR   0.008   0.001   TYR A  52 
 ARG   0.005   0.000   ARG G 134 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.749 
Fit side-chains
REVERT: G  164 MET cc_start: 0.5417 (ptm) cc_final: 0.4690 (ptm)
  outliers start: 16
  outliers final: 16
  residues processed: 75
  average time/residue: 0.1847
  time to fit residues: 19.1451
Evaluate side-chains
  77 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  233 GLU
Chi-restraints excluded: chain F residue  242 THR
Chi-restraints excluded: chain F residue  309 LEU
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  145 SER
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  150 THR
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  210 THR
Chi-restraints excluded: chain G residue  236 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    9.9990
   chunk 56 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 46 optimal weight:    5.9990
   chunk 57 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 48 optimal weight:    6.9990
   overall best weight:    3.9388

-------------------------------------------------------------------------------
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 = 0.3759 r_free = 0.3759 target = 0.163058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.114115 restraints weight = 7119.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 1.88
r_work: 0.2981 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.065   6260  Z= 0.494
  Angle     :  0.633   5.936   8481  Z= 0.335
  Chirality :  0.051   0.209    989
  Planarity :  0.004   0.054   1069
  Dihedral  : 13.152 150.099    937
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 16.40 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.29), residues: 788
  helix:  1.03 (0.29), residues: 305
  sheet:  0.64 (0.41), residues: 141
  loop : -0.98 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP F 308 
 HIS   0.005   0.002   HIS G  97 
 PHE   0.011   0.002   PHE F 260 
 TYR   0.013   0.002   TYR F 293 
 ARG   0.007   0.001   ARG G 134 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 57
  time to evaluate  : 0.758 
Fit side-chains
REVERT: B   33 TYR cc_start: 0.5215 (OUTLIER) cc_final: 0.4634 (p90)
REVERT: F  259 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8133 (mt-10)
REVERT: G  159 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7896 (mm)
REVERT: G  164 MET cc_start: 0.4824 (ptm) cc_final: 0.4417 (ptm)
  outliers start: 29
  outliers final: 21
  residues processed: 80
  average time/residue: 0.1866
  time to fit residues: 20.1484
Evaluate side-chains
  78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 54
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  150 THR
Chi-restraints excluded: chain F residue  201 VAL
Chi-restraints excluded: chain F residue  202 MET
Chi-restraints excluded: chain F residue  242 THR
Chi-restraints excluded: chain F residue  259 GLU
Chi-restraints excluded: chain F residue  309 LEU
Chi-restraints excluded: chain F residue  315 THR
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  145 SER
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  150 THR
Chi-restraints excluded: chain G residue  159 ILE
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  172 SER
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  210 THR
Chi-restraints excluded: chain G residue  236 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0770
   chunk 49 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.3142

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

Flipped N/Q/H residues before XYZ refinement:
F 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.166067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.115669 restraints weight = 6979.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.01
r_work: 0.3022 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6260  Z= 0.205
  Angle     :  0.481   4.452   8481  Z= 0.263
  Chirality :  0.045   0.164    989
  Planarity :  0.003   0.049   1069
  Dihedral  : 12.876 142.902    937
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 17.35 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.29), residues: 788
  helix:  1.14 (0.29), residues: 317
  sheet:  1.00 (0.44), residues: 124
  loop : -0.77 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP F 308 
 HIS   0.002   0.001   HIS G  97 
 PHE   0.009   0.001   PHE F 217 
 TYR   0.008   0.001   TYR F 291 
 ARG   0.006   0.000   ARG G 134 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 64
  time to evaluate  : 0.692 
Fit side-chains
REVERT: F  161 ASP cc_start: 0.7959 (m-30) cc_final: 0.7529 (m-30)
REVERT: F  259 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8054 (mt-10)
REVERT: G  159 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7916 (mm)
REVERT: G  164 MET cc_start: 0.4757 (ptm) cc_final: 0.4407 (ptm)
  outliers start: 25
  outliers final: 18
  residues processed: 84
  average time/residue: 0.1898
  time to fit residues: 21.4134
Evaluate side-chains
  79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  150 THR
Chi-restraints excluded: chain F residue  242 THR
Chi-restraints excluded: chain F residue  259 GLU
Chi-restraints excluded: chain F residue  309 LEU
Chi-restraints excluded: chain F residue  315 THR
Chi-restraints excluded: chain G residue   27 MET
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  145 SER
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  150 THR
Chi-restraints excluded: chain G residue  159 ILE
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  172 SER
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  210 THR
Chi-restraints excluded: chain G residue  236 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 75 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3806 r_free = 0.3806 target = 0.167425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.117830 restraints weight = 6923.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.21
r_work: 0.3038 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6260  Z= 0.176
  Angle     :  0.454   4.408   8481  Z= 0.250
  Chirality :  0.044   0.157    989
  Planarity :  0.003   0.052   1069
  Dihedral  : 12.718 140.863    937
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.45 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.30), residues: 788
  helix:  1.34 (0.30), residues: 317
  sheet:  1.16 (0.45), residues: 126
  loop : -0.76 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP F 308 
 HIS   0.002   0.001   HIS G  97 
 PHE   0.008   0.001   PHE F 217 
 TYR   0.008   0.001   TYR F 271 
 ARG   0.007   0.000   ARG G 134 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 0.716 
Fit side-chains
REVERT: F  161 ASP cc_start: 0.7915 (m-30) cc_final: 0.7477 (m-30)
REVERT: F  259 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8055 (mt-10)
REVERT: G  164 MET cc_start: 0.4873 (ptm) cc_final: 0.4476 (ptm)
  outliers start: 21
  outliers final: 15
  residues processed: 78
  average time/residue: 0.1608
  time to fit residues: 17.4496
Evaluate side-chains
  74 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  150 THR
Chi-restraints excluded: chain F residue  242 THR
Chi-restraints excluded: chain F residue  259 GLU
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  145 SER
Chi-restraints excluded: chain G residue  150 THR
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  172 SER
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  210 THR
Chi-restraints excluded: chain G residue  236 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:   30.0000
   chunk 55 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 15 optimal weight:   10.0000
   chunk 68 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.9588

-------------------------------------------------------------------------------
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 = 0.3766 r_free = 0.3766 target = 0.163620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.108343 restraints weight = 7045.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 1.77
r_work: 0.2987 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   6260  Z= 0.376
  Angle     :  0.560   5.318   8481  Z= 0.300
  Chirality :  0.048   0.161    989
  Planarity :  0.004   0.051   1069
  Dihedral  : 13.112 144.556    937
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 18.77 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.29), residues: 788
  helix:  1.28 (0.29), residues: 305
  sheet:  0.67 (0.41), residues: 139
  loop : -0.93 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP F 308 
 HIS   0.004   0.001   HIS G  97 
 PHE   0.009   0.002   PHE F 260 
 TYR   0.010   0.001   TYR A  52 
 ARG   0.006   0.001   ARG G 134 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 59
  time to evaluate  : 0.569 
Fit side-chains
REVERT: B   33 TYR cc_start: 0.4718 (OUTLIER) cc_final: 0.4128 (p90)
REVERT: F  161 ASP cc_start: 0.7980 (m-30) cc_final: 0.7509 (m-30)
REVERT: F  259 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8042 (mt-10)
REVERT: G  159 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7944 (mm)
REVERT: G  164 MET cc_start: 0.4995 (ptm) cc_final: 0.4596 (ptm)
  outliers start: 23
  outliers final: 17
  residues processed: 77
  average time/residue: 0.1662
  time to fit residues: 17.7982
Evaluate side-chains
  76 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 56
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  150 THR
Chi-restraints excluded: chain F residue  242 THR
Chi-restraints excluded: chain F residue  259 GLU
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  114 LEU
Chi-restraints excluded: chain G residue  145 SER
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  150 THR
Chi-restraints excluded: chain G residue  159 ILE
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  210 THR
Chi-restraints excluded: chain G residue  236 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 40 optimal weight:   10.0000
   chunk 75 optimal weight:    0.0030
   chunk 72 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 3 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.9998

-------------------------------------------------------------------------------
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 = 0.3775 r_free = 0.3775 target = 0.164533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.115693 restraints weight = 6928.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.87
r_work: 0.3021 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6260  Z= 0.276
  Angle     :  0.504   4.760   8481  Z= 0.273
  Chirality :  0.046   0.154    989
  Planarity :  0.003   0.050   1069
  Dihedral  : 13.005 141.964    937
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 18.77 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.30), residues: 788
  helix:  1.36 (0.29), residues: 305
  sheet:  0.65 (0.42), residues: 139
  loop : -0.90 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP F 308 
 HIS   0.003   0.001   HIS G  97 
 PHE   0.009   0.001   PHE B  15 
 TYR   0.008   0.001   TYR A  52 
 ARG   0.008   0.001   ARG G 134 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 60
  time to evaluate  : 0.693 
Fit side-chains
REVERT: B   33 TYR cc_start: 0.4622 (OUTLIER) cc_final: 0.4172 (p90)
REVERT: F  161 ASP cc_start: 0.7955 (m-30) cc_final: 0.7468 (m-30)
REVERT: F  259 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8020 (mt-10)
REVERT: G  159 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7848 (mm)
REVERT: G  164 MET cc_start: 0.4758 (ptm) cc_final: 0.4395 (ptm)
  outliers start: 25
  outliers final: 20
  residues processed: 79
  average time/residue: 0.1636
  time to fit residues: 17.9026
Evaluate side-chains
  80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 57
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  150 THR
Chi-restraints excluded: chain F residue  201 VAL
Chi-restraints excluded: chain F residue  202 MET
Chi-restraints excluded: chain F residue  242 THR
Chi-restraints excluded: chain F residue  259 GLU
Chi-restraints excluded: chain G residue   27 MET
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  114 LEU
Chi-restraints excluded: chain G residue  145 SER
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  150 THR
Chi-restraints excluded: chain G residue  159 ILE
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  210 THR
Chi-restraints excluded: chain G residue  236 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 73 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 57 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0870
   chunk 52 optimal weight:    0.7980
   chunk 6 optimal weight:    9.9990
   overall best weight:    1.5764

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

Flipped N/Q/H residues before XYZ refinement:
** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.165624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.116281 restraints weight = 7053.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 1.94
r_work: 0.3020 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6260  Z= 0.231
  Angle     :  0.485   5.720   8481  Z= 0.263
  Chirality :  0.045   0.153    989
  Planarity :  0.003   0.049   1069
  Dihedral  : 12.909 140.837    937
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.77 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.30), residues: 788
  helix:  1.46 (0.30), residues: 305
  sheet:  0.73 (0.42), residues: 139
  loop : -0.83 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP F 308 
 HIS   0.002   0.001   HIS G  97 
 PHE   0.010   0.001   PHE B  15 
 TYR   0.007   0.001   TYR A  52 
 ARG   0.008   0.000   ARG G 134 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 61
  time to evaluate  : 0.676 
Fit side-chains
REVERT: F  161 ASP cc_start: 0.7934 (m-30) cc_final: 0.7487 (m-30)
REVERT: F  259 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8033 (mt-10)
REVERT: G  159 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7860 (mm)
REVERT: G  164 MET cc_start: 0.4875 (ptm) cc_final: 0.4508 (ptm)
  outliers start: 22
  outliers final: 20
  residues processed: 77
  average time/residue: 0.1763
  time to fit residues: 18.5006
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 59
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  150 THR
Chi-restraints excluded: chain F residue  202 MET
Chi-restraints excluded: chain F residue  242 THR
Chi-restraints excluded: chain F residue  259 GLU
Chi-restraints excluded: chain G residue   27 MET
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  114 LEU
Chi-restraints excluded: chain G residue  145 SER
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  150 THR
Chi-restraints excluded: chain G residue  159 ILE
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  172 SER
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  210 THR
Chi-restraints excluded: chain G residue  236 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   chunk 58 optimal weight:    8.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.161844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.112203 restraints weight = 7095.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 1.96
r_work: 0.2973 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.077   6260  Z= 0.455
  Angle     :  0.611   9.807   8481  Z= 0.323
  Chirality :  0.050   0.185    989
  Planarity :  0.004   0.051   1069
  Dihedral  : 13.217 144.875    937
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 18.61 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.29), residues: 788
  helix:  1.07 (0.29), residues: 305
  sheet:  0.49 (0.42), residues: 139
  loop : -1.05 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP F 308 
 HIS   0.003   0.001   HIS G  97 
 PHE   0.012   0.002   PHE B  15 
 TYR   0.009   0.001   TYR A  52 
 ARG   0.009   0.001   ARG G 134 

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 56
  time to evaluate  : 0.692 
Fit side-chains
REVERT: B   33 TYR cc_start: 0.4270 (OUTLIER) cc_final: 0.3876 (p90)
REVERT: F  259 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8078 (mt-10)
REVERT: G  159 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7893 (mm)
REVERT: G  202 MET cc_start: 0.6675 (mtp) cc_final: 0.5993 (mmt)
  outliers start: 26
  outliers final: 21
  residues processed: 76
  average time/residue: 0.1605
  time to fit residues: 17.0149
Evaluate side-chains
  80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 56
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  150 THR
Chi-restraints excluded: chain F residue  201 VAL
Chi-restraints excluded: chain F residue  202 MET
Chi-restraints excluded: chain F residue  242 THR
Chi-restraints excluded: chain F residue  259 GLU
Chi-restraints excluded: chain G residue   69 SER
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  114 LEU
Chi-restraints excluded: chain G residue  145 SER
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  150 THR
Chi-restraints excluded: chain G residue  159 ILE
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  172 SER
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  210 THR
Chi-restraints excluded: chain G residue  236 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 6 optimal weight:   20.0000
   chunk 26 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0370
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.0862

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

Flipped N/Q/H residues before XYZ refinement:
** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.165542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.116552 restraints weight = 7039.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 1.93
r_work: 0.3026 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6260  Z= 0.193
  Angle     :  0.489   8.841   8481  Z= 0.265
  Chirality :  0.044   0.155    989
  Planarity :  0.003   0.049   1069
  Dihedral  : 12.920 139.464    937
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.24 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.30), residues: 788
  helix:  1.43 (0.30), residues: 305
  sheet:  0.63 (0.42), residues: 139
  loop : -0.86 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP F 308 
 HIS   0.002   0.001   HIS F  97 
 PHE   0.010   0.001   PHE B  15 
 TYR   0.008   0.001   TYR G  65 
 ARG   0.009   0.000   ARG G 134 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3435.35 seconds
wall clock time: 61 minutes 33.89 seconds (3693.89 seconds total)