Starting phenix.real_space_refine
on Fri Aug 22 17:06:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gmt_34153/08_2025/8gmt_34153.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gmt_34153/08_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_34153/08_2025/8gmt_34153.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gmt_34153/08_2025/8gmt_34153.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gmt_34153/08_2025/8gmt_34153.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gmt_34153/08_2025/8gmt_34153.cif"
  }
  resolution = 3.31
  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=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.88, per 1000 atoms: 0.30
  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: 0.54
  Conformation dependent library (CDL) restraints added in 373.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.26
  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: 1.07

  Time building geometry restraints manager: 0.73 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:             0.920
  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:          0.090
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.390
  Find NCS groups from input model:        0.090
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.890
-------------------------------------------------------------------------------
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= 0.144
  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 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:  1.01 (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
 ARG   0.008   0.000   ARG G 134 
 TYR   0.026   0.001   TYR B  33 
 PHE   0.008   0.001   PHE A 128 
 TRP   0.065   0.005   TRP F 308 
 HIS   0.002   0.001   HIS G  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6260)
  covalent geometry    : angle       0.51901 ( 8481)
  hydrogen bonds       : bond        0.16516 (  309)
  hydrogen bonds       : angle       7.25017 (  900)

*********************** 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  : 0.231 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 64
  average time/residue: 0.0891
  time to fit residues: 7.6667
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  : 0.250 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.1980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    4.0388

-------------------------------------------------------------------------------
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 = 0.3767 r_free = 0.3767 target = 0.163774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.112498 restraints weight = 7021.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 1.63
r_work: 0.3015 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.053   6260  Z= 0.317
  Angle     :  0.659   5.630   8481  Z= 0.353
  Chirality :  0.051   0.184    989
  Planarity :  0.005   0.067   1069
  Dihedral  : 13.166 148.706    937
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 6.94
  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 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:  0.43 (0.29), residues: 788
  helix:  1.18 (0.29), residues: 305
  sheet:  0.70 (0.40), residues: 147
  loop : -0.68 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 176 
 TYR   0.012   0.002   TYR A  52 
 PHE   0.015   0.002   PHE F 217 
 TRP   0.033   0.004   TRP F 308 
 HIS   0.004   0.001   HIS G  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00756 ( 6260)
  covalent geometry    : angle       0.65901 ( 8481)
  hydrogen bonds       : bond        0.04257 (  309)
  hydrogen bonds       : angle       5.64871 (  900)

*********************** 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  : 0.192 
Fit side-chains
REVERT: F  203 PHE cc_start: 0.6271 (t80) cc_final: 0.5923 (t80)
REVERT: G  164 MET cc_start: 0.4816 (ptm) cc_final: 0.4168 (ptm)
  outliers start: 22
  outliers final: 16
  residues processed: 75
  average time/residue: 0.0715
  time to fit residues: 7.3477
Evaluate side-chains
  73 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
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 6 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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 = 0.3789 r_free = 0.3789 target = 0.165858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.115717 restraints weight = 6964.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 1.78
r_work: 0.3022 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6260  Z= 0.174
  Angle     :  0.505   4.686   8481  Z= 0.277
  Chirality :  0.046   0.175    989
  Planarity :  0.004   0.055   1069
  Dihedral  : 12.909 146.059    937
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.51 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.48 (0.29), residues: 788
  helix:  1.13 (0.29), residues: 317
  sheet:  0.88 (0.43), residues: 129
  loop : -0.63 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G 134 
 TYR   0.008   0.001   TYR A  52 
 PHE   0.010   0.001   PHE F 217 
 TRP   0.031   0.003   TRP F 308 
 HIS   0.002   0.001   HIS G  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 6260)
  covalent geometry    : angle       0.50480 ( 8481)
  hydrogen bonds       : bond        0.03530 (  309)
  hydrogen bonds       : angle       5.28998 (  900)

*********************** 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
  80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.249 
Fit side-chains
REVERT: G  159 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7909 (mm)
REVERT: G  164 MET cc_start: 0.4690 (ptm) cc_final: 0.4030 (ptm)
  outliers start: 18
  outliers final: 17
  residues processed: 74
  average time/residue: 0.0753
  time to fit residues: 7.7595
Evaluate side-chains
  76 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
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  201 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  159 ILE
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 36 optimal weight:    2.9990
   chunk 41 optimal weight:    8.9990
   chunk 67 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 9 optimal weight:    6.9990
   chunk 73 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   overall best weight:    2.1386

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.166128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.111687 restraints weight = 6999.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.71
r_work: 0.3017 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6260  Z= 0.191
  Angle     :  0.516   4.923   8481  Z= 0.279
  Chirality :  0.046   0.170    989
  Planarity :  0.004   0.052   1069
  Dihedral  : 12.893 146.399    937
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 16.25 %
    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 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:  0.50 (0.30), residues: 788
  helix:  1.40 (0.30), residues: 305
  sheet:  0.58 (0.41), residues: 143
  loop : -0.75 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G 134 
 TYR   0.012   0.001   TYR F 293 
 PHE   0.008   0.001   PHE F 217 
 TRP   0.031   0.003   TRP F 308 
 HIS   0.003   0.001   HIS G  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 6260)
  covalent geometry    : angle       0.51584 ( 8481)
  hydrogen bonds       : bond        0.03430 (  309)
  hydrogen bonds       : angle       5.19166 (  900)

*********************** 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
  91 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 61
  time to evaluate  : 0.276 
Fit side-chains
REVERT: B   33 TYR cc_start: 0.5223 (OUTLIER) cc_final: 0.4645 (p90)
REVERT: F  259 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8048 (mt-10)
REVERT: G  159 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7942 (mm)
REVERT: G  164 MET cc_start: 0.4791 (ptm) cc_final: 0.4401 (ptm)
  outliers start: 30
  outliers final: 23
  residues processed: 84
  average time/residue: 0.0784
  time to fit residues: 8.8885
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  : 0.202 
-------------------------------------------------------------------------------
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   71 LEU
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  233 GLU
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 23 optimal weight:    4.9990
   chunk 60 optimal weight:    0.2980
   chunk 41 optimal weight:    9.9990
   chunk 69 optimal weight:    0.0980
   chunk 57 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 44 optimal weight:    9.9990
   chunk 11 optimal weight:    9.9990
   chunk 37 optimal weight:    0.0000
   chunk 13 optimal weight:    8.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.3984

-------------------------------------------------------------------------------
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 = 0.3843 r_free = 0.3843 target = 0.170836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.121849 restraints weight = 7036.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 2.14
r_work: 0.3071 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6260  Z= 0.096
  Angle     :  0.440   4.145   8481  Z= 0.243
  Chirality :  0.043   0.156    989
  Planarity :  0.003   0.046   1069
  Dihedral  : 12.542 140.234    937
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 19.24 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.68 (0.30), residues: 788
  helix:  1.42 (0.30), residues: 317
  sheet:  0.75 (0.42), residues: 143
  loop : -0.61 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G 134 
 TYR   0.009   0.001   TYR F 271 
 PHE   0.008   0.001   PHE F 217 
 TRP   0.031   0.002   TRP F 308 
 HIS   0.002   0.000   HIS G  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 6260)
  covalent geometry    : angle       0.44023 ( 8481)
  hydrogen bonds       : bond        0.02890 (  309)
  hydrogen bonds       : angle       4.95755 (  900)

*********************** 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
  86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.271 
Fit side-chains
REVERT: F   19 LYS cc_start: 0.8528 (ttmt) cc_final: 0.7726 (mmpt)
REVERT: F  161 ASP cc_start: 0.8006 (m-30) cc_final: 0.7502 (m-30)
REVERT: F  259 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8025 (mt-10)
REVERT: G  164 MET cc_start: 0.5380 (ptm) cc_final: 0.5042 (ptm)
  outliers start: 18
  outliers final: 10
  residues processed: 83
  average time/residue: 0.0743
  time to fit residues: 8.3284
Evaluate side-chains
  72 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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  146 VAL
Chi-restraints excluded: chain F residue  242 THR
Chi-restraints excluded: chain F residue  259 GLU
Chi-restraints excluded: chain F residue  315 THR
Chi-restraints excluded: chain G residue  145 SER
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  172 SER
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 15 optimal weight:    9.9990
   chunk 56 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   overall best weight:    1.4182

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.167485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.118156 restraints weight = 7037.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 1.86
r_work: 0.3037 rms_B_bonded: 2.51 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: 0.7886
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6260  Z= 0.142
  Angle     :  0.474   4.560   8481  Z= 0.257
  Chirality :  0.045   0.206    989
  Planarity :  0.003   0.052   1069
  Dihedral  : 12.650 141.651    936
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 18.45 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.65 (0.30), residues: 788
  helix:  1.40 (0.30), residues: 317
  sheet:  0.73 (0.42), residues: 143
  loop : -0.62 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G 134 
 TYR   0.009   0.001   TYR A  52 
 PHE   0.007   0.001   PHE F 217 
 TRP   0.034   0.002   TRP F 308 
 HIS   0.003   0.001   HIS G  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6260)
  covalent geometry    : angle       0.47428 ( 8481)
  hydrogen bonds       : bond        0.03054 (  309)
  hydrogen bonds       : angle       4.90451 (  900)

*********************** 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: 23
    poor density    : 61
  time to evaluate  : 0.230 
Fit side-chains
REVERT: F  161 ASP cc_start: 0.8034 (m-30) cc_final: 0.7494 (m-30)
REVERT: F  259 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8054 (mt-10)
REVERT: G  164 MET cc_start: 0.4822 (ptm) cc_final: 0.4454 (ptm)
  outliers start: 23
  outliers final: 15
  residues processed: 79
  average time/residue: 0.0677
  time to fit residues: 7.4209
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  : 0.210 
-------------------------------------------------------------------------------
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  114 LEU
Chi-restraints excluded: chain G residue  145 SER
Chi-restraints excluded: chain G residue  146 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 40 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 59 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3817 r_free = 0.3817 target = 0.168280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.120009 restraints weight = 6958.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.85
r_work: 0.3049 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6260  Z= 0.122
  Angle     :  0.449   4.166   8481  Z= 0.245
  Chirality :  0.044   0.168    989
  Planarity :  0.003   0.049   1069
  Dihedral  : 12.634 140.388    936
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 19.40 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.71 (0.30), residues: 788
  helix:  1.44 (0.30), residues: 317
  sheet:  0.77 (0.42), residues: 143
  loop : -0.59 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G 134 
 TYR   0.007   0.001   TYR A  52 
 PHE   0.008   0.001   PHE B  15 
 TRP   0.041   0.003   TRP F 308 
 HIS   0.002   0.001   HIS G  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6260)
  covalent geometry    : angle       0.44935 ( 8481)
  hydrogen bonds       : bond        0.02874 (  309)
  hydrogen bonds       : angle       4.84073 (  900)

*********************** 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
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.167 
Fit side-chains
REVERT: F   19 LYS cc_start: 0.8533 (ttmt) cc_final: 0.7716 (mmpt)
REVERT: F  161 ASP cc_start: 0.8012 (m-30) cc_final: 0.7504 (m-30)
REVERT: F  259 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7978 (mt-10)
REVERT: G  164 MET cc_start: 0.4855 (ptm) cc_final: 0.4176 (ptm)
  outliers start: 16
  outliers final: 15
  residues processed: 76
  average time/residue: 0.0716
  time to fit residues: 7.4612
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  : 0.248 
-------------------------------------------------------------------------------
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  242 THR
Chi-restraints excluded: chain F residue  259 GLU
Chi-restraints excluded: chain F residue  326 LEU
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  162 SER
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 65 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 74 optimal weight:    9.9990
   chunk 47 optimal weight:    0.1980
   chunk 33 optimal weight:    4.9990
   chunk 44 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 40 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   overall best weight:    3.6388

-------------------------------------------------------------------------------
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 = 0.162973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.111106 restraints weight = 7104.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 1.99
r_work: 0.2993 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.081   6260  Z= 0.287
  Angle     :  0.596   5.406   8481  Z= 0.317
  Chirality :  0.050   0.235    989
  Planarity :  0.004   0.051   1069
  Dihedral  : 13.168 145.511    936
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.61 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.27 (0.29), residues: 788
  helix:  1.17 (0.29), residues: 305
  sheet:  0.67 (0.42), residues: 137
  loop : -0.91 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G 134 
 TYR   0.012   0.001   TYR A  52 
 PHE   0.011   0.002   PHE F 260 
 TRP   0.041   0.003   TRP F 308 
 HIS   0.003   0.001   HIS G  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00685 ( 6260)
  covalent geometry    : angle       0.59566 ( 8481)
  hydrogen bonds       : bond        0.03652 (  309)
  hydrogen bonds       : angle       5.19801 (  900)

*********************** 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
  79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 57
  time to evaluate  : 0.150 
Fit side-chains
REVERT: B   33 TYR cc_start: 0.4795 (OUTLIER) cc_final: 0.4284 (p90)
REVERT: A   66 ILE cc_start: 0.5726 (mt) cc_final: 0.5482 (mt)
REVERT: F  259 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8034 (mt-10)
REVERT: G  159 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7934 (mm)
REVERT: G  202 MET cc_start: 0.6693 (mtp) cc_final: 0.6027 (mmt)
  outliers start: 22
  outliers final: 17
  residues processed: 74
  average time/residue: 0.0742
  time to fit residues: 7.7520
Evaluate side-chains
  77 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 21 optimal weight:    0.3980
   chunk 67 optimal weight:    0.9980
   chunk 74 optimal weight:    9.9990
   chunk 60 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 47 optimal weight:    7.9990
   chunk 46 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.167585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.119424 restraints weight = 7001.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 1.81
r_work: 0.3067 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2084

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= 0.112
  Angle     :  0.457   4.688   8481  Z= 0.252
  Chirality :  0.044   0.191    989
  Planarity :  0.003   0.048   1069
  Dihedral  : 12.751 138.206    936
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.56 %
    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 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:  0.56 (0.30), residues: 788
  helix:  1.29 (0.30), residues: 317
  sheet:  0.85 (0.42), residues: 137
  loop : -0.70 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G 134 
 TYR   0.007   0.001   TYR G  65 
 PHE   0.009   0.001   PHE B  15 
 TRP   0.041   0.003   TRP F 308 
 HIS   0.002   0.001   HIS A 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6260)
  covalent geometry    : angle       0.45736 ( 8481)
  hydrogen bonds       : bond        0.02900 (  309)
  hydrogen bonds       : angle       4.90197 (  900)

*********************** 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: 17
    poor density    : 66
  time to evaluate  : 0.238 
Fit side-chains
REVERT: F  259 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7970 (mt-10)
  outliers start: 17
  outliers final: 13
  residues processed: 80
  average time/residue: 0.0798
  time to fit residues: 8.6546
Evaluate side-chains
  76 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
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  242 THR
Chi-restraints excluded: chain F residue  259 GLU
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  162 SER
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 27 optimal weight:    0.2980
   chunk 8 optimal weight:    7.9990
   chunk 74 optimal weight:    9.9990
   chunk 26 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0870
   chunk 35 optimal weight:    0.0170
   chunk 52 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.3596

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

Flipped N/Q/H residues before XYZ refinement:
G  78 GLN
G 118 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.169939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.121929 restraints weight = 6962.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.12
r_work: 0.3081 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   6260  Z= 0.098
  Angle     :  0.471  10.081   8481  Z= 0.252
  Chirality :  0.043   0.151    989
  Planarity :  0.003   0.048   1069
  Dihedral  : 12.432 136.058    936
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 20.50 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.76 (0.30), residues: 788
  helix:  1.45 (0.30), residues: 317
  sheet:  0.84 (0.43), residues: 143
  loop : -0.54 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G 134 
 TYR   0.007   0.001   TYR G  65 
 PHE   0.013   0.001   PHE G 203 
 TRP   0.039   0.003   TRP F 308 
 HIS   0.002   0.001   HIS G  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 6260)
  covalent geometry    : angle       0.47072 ( 8481)
  hydrogen bonds       : bond        0.02693 (  309)
  hydrogen bonds       : angle       4.73104 (  900)

********************** 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
  76 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.243 
Fit side-chains
REVERT: F   19 LYS cc_start: 0.8550 (ttmt) cc_final: 0.7801 (mmpt)
REVERT: F  161 ASP cc_start: 0.7963 (m-30) cc_final: 0.7492 (m-30)
REVERT: F  259 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7973 (mt-10)
  outliers start: 10
  outliers final: 9
  residues processed: 74
  average time/residue: 0.0881
  time to fit residues: 8.6637
Evaluate side-chains
  74 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
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  146 VAL
Chi-restraints excluded: chain F residue  242 THR
Chi-restraints excluded: chain F residue  259 GLU
Chi-restraints excluded: chain G residue  114 LEU
Chi-restraints excluded: chain G residue  145 SER
Chi-restraints excluded: chain G residue  162 SER
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 17 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 50 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 75 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    2.8786

-------------------------------------------------------------------------------
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 = 0.164616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.114711 restraints weight = 7003.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 2.04
r_work: 0.2998 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067   6260  Z= 0.231
  Angle     :  0.557   8.848   8481  Z= 0.295
  Chirality :  0.048   0.222    989
  Planarity :  0.004   0.050   1069
  Dihedral  : 12.964 142.633    936
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.87 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.54 (0.30), residues: 788
  helix:  1.36 (0.29), residues: 305
  sheet:  0.83 (0.43), residues: 137
  loop : -0.73 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G 134 
 TYR   0.009   0.001   TYR A  52 
 PHE   0.012   0.002   PHE G 203 
 TRP   0.038   0.003   TRP F 308 
 HIS   0.002   0.001   HIS G  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 6260)
  covalent geometry    : angle       0.55743 ( 8481)
  hydrogen bonds       : bond        0.03365 (  309)
  hydrogen bonds       : angle       5.03917 (  900)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1643.28 seconds
wall clock time: 28 minutes 44.41 seconds (1724.41 seconds total)