Starting phenix.real_space_refine
on Fri Aug 22 15:55:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gej_29972/08_2025/8gej_29972.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gej_29972/08_2025/8gej_29972.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gej_29972/08_2025/8gej_29972.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gej_29972/08_2025/8gej_29972.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gej_29972/08_2025/8gej_29972.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gej_29972/08_2025/8gej_29972.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       9      5.16       5
     C    3368      2.51       5
     N    1029      2.21       5
     O    1030      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  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: 5436
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 1718
          Classifications: {'peptide': 313}
          Incomplete info: {'truncation_to_alanine': 247}
          Link IDs: {'PTRANS': 9, 'TRANS': 303}
          Chain breaks: 10
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 928
          Unresolved non-hydrogen angles: 1174
          Unresolved non-hydrogen dihedrals: 762
          Unresolved non-hydrogen chiralities: 74
          Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 23, 'ASN:plan1': 16, 'GLU:plan': 25, 'ASP:plan': 20, 'TYR:plan': 7, 'HIS:plan': 2, 'PHE:plan': 11, 'TRP:plan': 4}
          Unresolved non-hydrogen planarities: 548
    Chain: "B"
      Number of atoms: 1894
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 1894
          Classifications: {'peptide': 323}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 191}
          Link IDs: {'PTRANS': 5, 'TRANS': 317}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 601
          Unresolved non-hydrogen angles: 757
          Unresolved non-hydrogen dihedrals: 462
          Unresolved non-hydrogen chiralities: 66
          Planarities with less than four sites: {'ARG:plan': 18, 'GLN:plan1': 10, 'GLU:plan': 7, 'ASN:plan1': 14, 'ASP:plan': 25, 'HIS:plan': 2, 'PHE:plan': 3, 'TRP:plan': 1, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 315
    Chain: "G"
      Number of atoms: 232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 232
          Classifications: {'peptide': 44}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 2, 'TRANS': 41}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 116
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 97
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 62
    Chain: "R"
      Number of atoms: 1577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 1577
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 180}
          Link IDs: {'PTRANS': 6, 'TRANS': 263}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 625
          Unresolved non-hydrogen angles: 813
          Unresolved non-hydrogen dihedrals: 506
          Unresolved non-hydrogen chiralities: 91
          Planarities with less than four sites: {'TRP:plan': 3, 'PHE:plan': 12, 'ASN:plan1': 7, 'GLU:plan': 10, 'GLN:plan1': 8, 'TYR:plan': 7, 'ASP:plan': 5, 'ARG:plan': 4, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 281
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.46, per 1000 atoms: 0.27
  Number of scatterers: 5436
  At special positions: 0
  Unit cell: (66.78, 97.52, 127.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       9     16.00
     O    1030      8.00
     N    1029      7.00
     C    3368      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " distance=2.03

  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: 0.37
  Conformation dependent library (CDL) restraints added in 164.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1816

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      50.6% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 3.933A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 91 through 113
    Processing helix  chain 'A' and resid 125 through 134
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 156 through 165
      removed outlier: 3.571A  pdb=" N   ARG A 160 " --> pdb=" O   ASP A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 185
    Processing helix  chain 'A' and resid 232 through 238
      removed outlier: 3.708A  pdb=" N   GLN A 236 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   PHE A 238 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.521A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.590A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 4.407A  pdb=" N   ARG A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.815A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 388
      removed outlier: 3.767A  pdb=" N   GLN A 384 " --> pdb=" O   ARG A 380 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ARG A 385 " --> pdb=" O   ASP A 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 26
      removed outlier: 3.555A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 37
      removed outlier: 3.918A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   ASN B  36 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ILE B  37 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 14 through 24
      removed outlier: 3.913A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.928A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 96
      removed outlier: 3.910A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.718A  pdb=" N   PHE R 108 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA R 128 " --> pdb=" O   LEU R 124 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.211A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 5.098A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 160
    Processing helix  chain 'R' and resid 165 through 172
      removed outlier: 4.061A  pdb=" N   ILE R 169 " --> pdb=" O   SER R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 187
      removed outlier: 3.989A  pdb=" N   TYR R 185 " --> pdb=" O   ALA R 181 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 196 through 235
      removed outlier: 3.559A  pdb=" N   ILE R 201 " --> pdb=" O   GLN R 197 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA R 202 " --> pdb=" O   ALA R 198 " (cutoff:3.500A)
      removed outlier: 5.683A  pdb=" N   VAL R 210 " --> pdb=" O   VAL R 206 " (cutoff:3.500A)
      Proline residue:  R 211  - end of helix
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.763A  pdb=" N   ILE R 278 " --> pdb=" O   THR R 274 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 3.933A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 332 through 339
      removed outlier: 3.698A  pdb=" N   LEU R 339 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 211
      removed outlier: 5.930A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249
      removed outlier: 6.237A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 52
    Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 63
      removed outlier: 3.918A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105
      removed outlier: 3.506A  pdb=" N   CYS B 114 " --> pdb=" O   SER B 122 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 150 through 151
      removed outlier: 3.531A  pdb=" N   VAL B 158 " --> pdb=" O   ARG B 150 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 165 through 166
    Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 170
      removed outlier: 3.887A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.849A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 233 through 234
      removed outlier: 6.660A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.763A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   TRP B 297 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.078A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 315 through 320
      removed outlier: 6.909A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)

    362 hydrogen bonds defined for protein.
    1062 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.86

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 975
        1.31 -     1.43: 1459
        1.43 -     1.56: 3063
        1.56 -     1.69: 1
        1.69 -     1.81: 9
  Bond restraints: 5507
  Sorted by residual:
  bond pdb=" C   SER R 319 "
       pdb=" O   SER R 319 "
    ideal  model  delta    sigma   weight residual
    1.237  1.182  0.055 1.17e-02 7.31e+03 2.22e+01
  bond pdb=" CA  LEU R 310 "
       pdb=" C   LEU R 310 "
    ideal  model  delta    sigma   weight residual
    1.524  1.479  0.046 1.28e-02 6.10e+03 1.28e+01
  bond pdb=" CA  ILE R 314 "
       pdb=" C   ILE R 314 "
    ideal  model  delta    sigma   weight residual
    1.523  1.482  0.041 1.27e-02 6.20e+03 1.06e+01
  bond pdb=" CA  TYR R 316 "
       pdb=" C   TYR R 316 "
    ideal  model  delta    sigma   weight residual
    1.524  1.482  0.041 1.29e-02 6.01e+03 1.03e+01
  bond pdb=" CA  TRP R 313 "
       pdb=" C   TRP R 313 "
    ideal  model  delta    sigma   weight residual
    1.523  1.483  0.040 1.34e-02 5.57e+03 9.00e+00
  ... (remaining 5502 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 7466
        1.40 -     2.79: 107
        2.79 -     4.19: 29
        4.19 -     5.58: 13
        5.58 -     6.98: 2
  Bond angle restraints: 7617
  Sorted by residual:
  angle pdb=" N   ASN R 322 "
        pdb=" CA  ASN R 322 "
        pdb=" C   ASN R 322 "
      ideal   model   delta    sigma   weight residual
     113.16  106.18    6.98 1.42e+00 4.96e-01 2.41e+01
  angle pdb=" C   ILE R 314 "
        pdb=" N   GLY R 315 "
        pdb=" CA  GLY R 315 "
      ideal   model   delta    sigma   weight residual
     119.94  114.54    5.40 1.11e+00 8.12e-01 2.36e+01
  angle pdb=" C   ILE R 314 "
        pdb=" CA  ILE R 314 "
        pdb=" CB  ILE R 314 "
      ideal   model   delta    sigma   weight residual
     112.14  105.99    6.15 1.35e+00 5.49e-01 2.07e+01
  angle pdb=" C   ASN R 322 "
        pdb=" N   PRO R 323 "
        pdb=" CA  PRO R 323 "
      ideal   model   delta    sigma   weight residual
     119.05  123.62   -4.57 1.11e+00 8.12e-01 1.69e+01
  angle pdb=" N   LEU R 324 "
        pdb=" CA  LEU R 324 "
        pdb=" C   LEU R 324 "
      ideal   model   delta    sigma   weight residual
     111.28  107.39    3.89 1.09e+00 8.42e-01 1.27e+01
  ... (remaining 7612 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.88: 2928
        8.88 -    17.75: 115
       17.75 -    26.62: 56
       26.62 -    35.49: 19
       35.49 -    44.37: 10
  Dihedral angle restraints: 3128
    sinusoidal: 366
      harmonic: 2762
  Sorted by residual:
  dihedral pdb=" CA  SER B  74 "
           pdb=" C   SER B  74 "
           pdb=" N   GLN B  75 "
           pdb=" CA  GLN B  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.15   17.85     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  TRP B 169 "
           pdb=" C   TRP B 169 "
           pdb=" N   ASP B 170 "
           pdb=" CA  ASP B 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.51   15.49     0      5.00e+00 4.00e-02 9.60e+00
  dihedral pdb=" CA  HIS B  54 "
           pdb=" C   HIS B  54 "
           pdb=" N   LEU B  55 "
           pdb=" CA  LEU B  55 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.58  -14.42     0      5.00e+00 4.00e-02 8.32e+00
  ... (remaining 3125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 720
       0.042 -    0.085: 187
       0.085 -    0.127: 48
       0.127 -    0.170: 1
       0.170 -    0.212: 1
  Chirality restraints: 957
  Sorted by residual:
  chirality pdb=" CA  TYR R 316 "
            pdb=" N   TYR R 316 "
            pdb=" C   TYR R 316 "
            pdb=" CB  TYR R 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.54   -0.14 2.00e-01 2.50e+01 5.19e-01
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.75e-01
  ... (remaining 954 not shown)

  Planarity restraints: 1037
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 309 "    0.015 2.00e-02 2.50e+03   3.00e-02 9.03e+00
        pdb=" C   ILE R 309 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   ILE R 309 "    0.019 2.00e-02 2.50e+03
        pdb=" N   LEU R 310 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP R 313 "   -0.009 2.00e-02 2.50e+03   1.83e-02 3.35e+00
        pdb=" C   TRP R 313 "    0.032 2.00e-02 2.50e+03
        pdb=" O   TRP R 313 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ILE R 314 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 310 "    0.008 2.00e-02 2.50e+03   1.59e-02 2.53e+00
        pdb=" C   LEU R 310 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   LEU R 310 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LEU R 311 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1034 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 741
        2.75 -     3.29: 5574
        3.29 -     3.82: 8943
        3.82 -     4.36: 8305
        4.36 -     4.90: 14704
  Nonbonded interactions: 38267
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A  19 "
            pdb=" OG1 THR B  86 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" N   SER B 147 "
            pdb=" O   SER B 160 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   ASP B 228 "
            pdb=" N   ASP B 246 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" O   ASN B 155 "
            pdb=" N   ILE B 171 "
     model   vdw
     2.333 3.120
  ... (remaining 38262 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.430
  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:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     6.500
  Find NCS groups from input model:        0.040
  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:   10.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
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      :  0.004   0.055   5508  Z= 0.233
  Angle     :  0.501   6.976   7619  Z= 0.327
  Chirality :  0.040   0.212    957
  Planarity :  0.003   0.036   1037
  Dihedral  :  8.378  44.368   1309
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.29), residues: 906
  helix:  2.79 (0.25), residues: 432
  sheet: -0.03 (0.56), residues: 106
  loop : -1.43 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 131 
 TYR   0.011   0.001   TYR A 147 
 PHE   0.010   0.001   PHE A 340 
 TRP   0.008   0.001   TRP B 297 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 5507)
  covalent geometry    : angle       0.50126 ( 7617)
  SS BOND              : bond        0.00315 (    1)
  SS BOND              : angle       0.87017 (    2)
  hydrogen bonds       : bond        0.16656 (  362)
  hydrogen bonds       : angle       6.29533 ( 1062)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.200 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0318
  time to fit residues: 2.0962
Evaluate side-chains
  30 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 53 optimal weight:    0.0570
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.8102

-------------------------------------------------------------------------------
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 = 0.3214 r_free = 0.3214 target = 0.063682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.057148 restraints weight = 41723.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.057903 restraints weight = 28202.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.058457 restraints weight = 20793.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.058811 restraints weight = 16362.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.059115 restraints weight = 13768.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.0910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5508  Z= 0.129
  Angle     :  0.404   5.439   7619  Z= 0.235
  Chirality :  0.039   0.123    957
  Planarity :  0.003   0.039   1037
  Dihedral  :  3.588  16.038    971
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.29), residues: 906
  helix:  2.40 (0.25), residues: 449
  sheet: -0.40 (0.53), residues: 114
  loop : -1.60 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  68 
 TYR   0.010   0.001   TYR A 147 
 PHE   0.016   0.001   PHE R 208 
 TRP   0.012   0.001   TRP B 297 
 HIS   0.008   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 5507)
  covalent geometry    : angle       0.40427 ( 7617)
  SS BOND              : bond        0.00069 (    1)
  SS BOND              : angle       0.12750 (    2)
  hydrogen bonds       : bond        0.03307 (  362)
  hydrogen bonds       : angle       4.33740 ( 1062)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.208 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0319
  time to fit residues: 2.1205
Evaluate side-chains
  30 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 89 optimal weight:    0.7980
   chunk 63 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 42 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 5 optimal weight:   20.0000
   chunk 81 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   chunk 33 optimal weight:    0.0470
   overall best weight:    3.1684

-------------------------------------------------------------------------------
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 = 0.3184 r_free = 0.3184 target = 0.062507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.056016 restraints weight = 41657.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.056779 restraints weight = 28338.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.057284 restraints weight = 20853.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.057655 restraints weight = 16506.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.057965 restraints weight = 13798.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5508  Z= 0.194
  Angle     :  0.439   5.364   7619  Z= 0.262
  Chirality :  0.040   0.120    957
  Planarity :  0.003   0.038   1037
  Dihedral  :  3.911  17.334    971
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.29), residues: 906
  helix:  2.38 (0.25), residues: 438
  sheet: -0.41 (0.53), residues: 114
  loop : -1.67 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  22 
 TYR   0.013   0.001   TYR A 147 
 PHE   0.016   0.002   PHE R 208 
 TRP   0.009   0.001   TRP B 297 
 HIS   0.004   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 5507)
  covalent geometry    : angle       0.43916 ( 7617)
  SS BOND              : bond        0.00303 (    1)
  SS BOND              : angle       0.65491 (    2)
  hydrogen bonds       : bond        0.03584 (  362)
  hydrogen bonds       : angle       4.44026 ( 1062)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.141 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0306
  time to fit residues: 2.0462
Evaluate side-chains
  31 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0670
   chunk 76 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 44 optimal weight:   10.0000
   chunk 70 optimal weight:    7.9990
   chunk 69 optimal weight:   20.0000
   chunk 35 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   chunk 13 optimal weight:   20.0000
   overall best weight:    0.9320

-------------------------------------------------------------------------------
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 = 0.3230 r_free = 0.3230 target = 0.064170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.057702 restraints weight = 41251.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.058466 restraints weight = 27590.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.058988 restraints weight = 20220.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.059416 restraints weight = 15974.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.059715 restraints weight = 13153.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5508  Z= 0.082
  Angle     :  0.367   5.323   7619  Z= 0.210
  Chirality :  0.039   0.122    957
  Planarity :  0.002   0.042   1037
  Dihedral  :  3.323  15.357    971
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.29), residues: 906
  helix:  2.64 (0.25), residues: 443
  sheet: -0.40 (0.53), residues: 110
  loop : -1.52 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  22 
 TYR   0.009   0.001   TYR R 219 
 PHE   0.021   0.001   PHE R 193 
 TRP   0.004   0.001   TRP R 158 
 HIS   0.001   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00153 ( 5507)
  covalent geometry    : angle       0.36675 ( 7617)
  SS BOND              : bond        0.00108 (    1)
  SS BOND              : angle       0.54912 (    2)
  hydrogen bonds       : bond        0.02670 (  362)
  hydrogen bonds       : angle       3.72167 ( 1062)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.219 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0296
  time to fit residues: 1.9904
Evaluate side-chains
  30 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 58 optimal weight:    1.9990
   chunk 7 optimal weight:   20.0000
   chunk 25 optimal weight:    0.2980
   chunk 59 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 17 optimal weight:    0.1980
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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 = 0.3214 r_free = 0.3214 target = 0.063605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.057111 restraints weight = 41916.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.057892 restraints weight = 28209.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.058434 restraints weight = 20572.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.058843 restraints weight = 16152.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.059153 restraints weight = 13314.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5508  Z= 0.116
  Angle     :  0.381   5.259   7619  Z= 0.221
  Chirality :  0.039   0.119    957
  Planarity :  0.002   0.039   1037
  Dihedral  :  3.366  15.372    971
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.29), residues: 906
  helix:  2.70 (0.25), residues: 442
  sheet: -0.18 (0.54), residues: 105
  loop : -1.67 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  22 
 TYR   0.009   0.001   TYR R 219 
 PHE   0.018   0.001   PHE R 208 
 TRP   0.005   0.001   TRP B 297 
 HIS   0.002   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 5507)
  covalent geometry    : angle       0.38052 ( 7617)
  SS BOND              : bond        0.00285 (    1)
  SS BOND              : angle       0.71126 (    2)
  hydrogen bonds       : bond        0.02778 (  362)
  hydrogen bonds       : angle       3.74136 ( 1062)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.241 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0325
  time to fit residues: 2.2262
Evaluate side-chains
  30 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9980
   chunk 89 optimal weight:    0.5980
   chunk 8 optimal weight:   30.0000
   chunk 62 optimal weight:    8.9990
   chunk 68 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 = 0.3222 r_free = 0.3222 target = 0.063883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.057414 restraints weight = 41391.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.058165 restraints weight = 27656.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.058689 restraints weight = 20416.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.059121 restraints weight = 16165.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.059446 restraints weight = 13218.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5508  Z= 0.104
  Angle     :  0.373   5.463   7619  Z= 0.216
  Chirality :  0.039   0.121    957
  Planarity :  0.002   0.040   1037
  Dihedral  :  3.316  15.364    971
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.29), residues: 906
  helix:  2.74 (0.25), residues: 443
  sheet: -0.06 (0.55), residues: 99
  loop : -1.57 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  22 
 TYR   0.010   0.001   TYR A 360 
 PHE   0.019   0.001   PHE R 208 
 TRP   0.006   0.001   TRP B 297 
 HIS   0.002   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 ( 5507)
  covalent geometry    : angle       0.37292 ( 7617)
  SS BOND              : bond        0.00250 (    1)
  SS BOND              : angle       0.74492 (    2)
  hydrogen bonds       : bond        0.02631 (  362)
  hydrogen bonds       : angle       3.61589 ( 1062)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.204 
Fit side-chains
REVERT: R  136 THR cc_start: 0.8256 (t) cc_final: 0.7943 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0341
  time to fit residues: 2.2872
Evaluate side-chains
  30 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   chunk 80 optimal weight:    0.0870
   chunk 79 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   overall best weight:    2.7564

-------------------------------------------------------------------------------
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 = 0.3191 r_free = 0.3191 target = 0.062733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.056226 restraints weight = 42348.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.056979 restraints weight = 28298.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.057510 restraints weight = 20865.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.057928 restraints weight = 16491.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.058217 restraints weight = 13636.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5508  Z= 0.171
  Angle     :  0.423   5.269   7619  Z= 0.251
  Chirality :  0.040   0.119    957
  Planarity :  0.003   0.039   1037
  Dihedral  :  3.735  16.861    971
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.29), residues: 906
  helix:  2.55 (0.25), residues: 435
  sheet: -0.26 (0.54), residues: 99
  loop : -1.58 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 342 
 TYR   0.013   0.001   TYR A 360 
 PHE   0.019   0.002   PHE R 208 
 TRP   0.013   0.001   TRP B 297 
 HIS   0.003   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 5507)
  covalent geometry    : angle       0.42226 ( 7617)
  SS BOND              : bond        0.00422 (    1)
  SS BOND              : angle       1.01785 (    2)
  hydrogen bonds       : bond        0.03216 (  362)
  hydrogen bonds       : angle       4.03145 ( 1062)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.208 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0331
  time to fit residues: 2.1856
Evaluate side-chains
  31 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 13 optimal weight:   20.0000
   chunk 20 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 1 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0270
   chunk 32 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    1.2046

-------------------------------------------------------------------------------
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 = 0.3224 r_free = 0.3224 target = 0.063916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.057420 restraints weight = 41330.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.058184 restraints weight = 27659.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.058711 restraints weight = 20334.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.059123 restraints weight = 16133.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.059407 restraints weight = 13340.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5508  Z= 0.091
  Angle     :  0.363   5.288   7619  Z= 0.209
  Chirality :  0.039   0.120    957
  Planarity :  0.002   0.040   1037
  Dihedral  :  3.321  15.161    971
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.29), residues: 906
  helix:  2.71 (0.25), residues: 443
  sheet: -0.32 (0.54), residues: 100
  loop : -1.56 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  22 
 TYR   0.010   0.001   TYR R 219 
 PHE   0.011   0.001   PHE A 246 
 TRP   0.008   0.001   TRP B 297 
 HIS   0.002   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00171 ( 5507)
  covalent geometry    : angle       0.36287 ( 7617)
  SS BOND              : bond        0.00241 (    1)
  SS BOND              : angle       0.85310 (    2)
  hydrogen bonds       : bond        0.02591 (  362)
  hydrogen bonds       : angle       3.63028 ( 1062)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.311 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0335
  time to fit residues: 2.2419
Evaluate side-chains
  30 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 17 optimal weight:    0.1980
   chunk 54 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 86 optimal weight:    8.9990
   chunk 52 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 69 optimal weight:   20.0000
   chunk 43 optimal weight:   20.0000
   chunk 82 optimal weight:    4.9990
   chunk 10 optimal weight:   20.0000
   overall best weight:    3.4388

-------------------------------------------------------------------------------
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 = 0.3178 r_free = 0.3178 target = 0.062230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.055747 restraints weight = 41951.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.056474 restraints weight = 28359.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.057006 restraints weight = 20965.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.057359 restraints weight = 16600.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.057661 restraints weight = 13971.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5508  Z= 0.214
  Angle     :  0.456   5.297   7619  Z= 0.274
  Chirality :  0.040   0.120    957
  Planarity :  0.003   0.038   1037
  Dihedral  :  3.966  18.142    971
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.29), residues: 906
  helix:  2.40 (0.25), residues: 435
  sheet: -0.43 (0.54), residues: 99
  loop : -1.65 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 283 
 TYR   0.016   0.002   TYR A 360 
 PHE   0.019   0.002   PHE R 208 
 TRP   0.015   0.001   TRP B 297 
 HIS   0.004   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 5507)
  covalent geometry    : angle       0.45610 ( 7617)
  SS BOND              : bond        0.00476 (    1)
  SS BOND              : angle       1.14058 (    2)
  hydrogen bonds       : bond        0.03461 (  362)
  hydrogen bonds       : angle       4.28337 ( 1062)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.154 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0333
  time to fit residues: 2.1195
Evaluate side-chains
  30 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 63 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9980
   chunk 52 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 72 optimal weight:    9.9990
   overall best weight:    3.5988

-------------------------------------------------------------------------------
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 = 0.3173 r_free = 0.3173 target = 0.062003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.055506 restraints weight = 42315.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.056222 restraints weight = 28446.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.056685 restraints weight = 21026.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.057097 restraints weight = 16970.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.057420 restraints weight = 14120.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5508  Z= 0.218
  Angle     :  0.471   5.291   7619  Z= 0.283
  Chirality :  0.041   0.120    957
  Planarity :  0.003   0.038   1037
  Dihedral  :  4.250  20.041    971
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.29), residues: 906
  helix:  2.01 (0.25), residues: 441
  sheet: -0.83 (0.53), residues: 101
  loop : -1.77 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  68 
 TYR   0.024   0.002   TYR R 209 
 PHE   0.019   0.002   PHE R 208 
 TRP   0.024   0.002   TRP B 297 
 HIS   0.004   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 5507)
  covalent geometry    : angle       0.47048 ( 7617)
  SS BOND              : bond        0.00497 (    1)
  SS BOND              : angle       1.25861 (    2)
  hydrogen bonds       : bond        0.03624 (  362)
  hydrogen bonds       : angle       4.54184 ( 1062)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.200 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0269
  time to fit residues: 1.7654
Evaluate side-chains
  29 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 78 optimal weight:    7.9990
   chunk 10 optimal weight:   30.0000
   chunk 32 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 50 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 55 optimal weight:    9.9990
   chunk 68 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 52 optimal weight:    8.9990
   chunk 46 optimal weight:    8.9990
   overall best weight:    3.2986

-------------------------------------------------------------------------------
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 = 0.3177 r_free = 0.3177 target = 0.062173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.055723 restraints weight = 41872.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.056462 restraints weight = 28357.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.056962 restraints weight = 20875.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.057309 restraints weight = 16515.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.057630 restraints weight = 13964.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5508  Z= 0.204
  Angle     :  0.456   5.327   7619  Z= 0.273
  Chirality :  0.040   0.119    957
  Planarity :  0.003   0.038   1037
  Dihedral  :  4.179  19.824    971
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.29), residues: 906
  helix:  1.94 (0.25), residues: 441
  sheet: -1.16 (0.52), residues: 106
  loop : -1.70 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  22 
 TYR   0.013   0.001   TYR A 147 
 PHE   0.020   0.002   PHE R 208 
 TRP   0.012   0.001   TRP B 297 
 HIS   0.004   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 5507)
  covalent geometry    : angle       0.45536 ( 7617)
  SS BOND              : bond        0.00548 (    1)
  SS BOND              : angle       1.25885 (    2)
  hydrogen bonds       : bond        0.03497 (  362)
  hydrogen bonds       : angle       4.50841 ( 1062)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 805.91 seconds
wall clock time: 14 minutes 29.73 seconds (869.73 seconds total)