Starting phenix.real_space_refine
on Thu Mar  6 07:53:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gej_29972/03_2025/8gej_29972.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gej_29972/03_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_29972/03_2025/8gej_29972.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gej_29972/03_2025/8gej_29972.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gej_29972/03_2025/8gej_29972.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gej_29972/03_2025/8gej_29972.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 16, 'TRP:plan': 4, 'ASP:plan': 20, 'PHE:plan': 11, 'GLU:plan': 25, 'ARG:plan': 23}
          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: {'GLN:plan1': 10, 'ASP:plan': 25, 'ASN:plan1': 14, 'TRP:plan': 1, 'HIS:plan': 2, 'ASN%COO:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 18}
          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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2}
          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: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 12, 'GLU:plan': 10, 'ARG:plan': 4}
          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: 4.01, per 1000 atoms: 0.74
  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: 1.87
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.70
  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: 1.77

  Time building geometry restraints manager: 1.79 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:             2.290
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.950
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.410
-------------------------------------------------------------------------------
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   5507  Z= 0.250
  Angle     :  0.501   6.976   7617  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (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
 TRP   0.008   0.001   TRP B 297 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.010   0.001   PHE A 340 
 TYR   0.011   0.001   TYR A 147 
 ARG   0.001   0.000   ARG R 131 

*********************** 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  : 0.579 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0783
  time to fit residues: 5.2149
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  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    8.9990
   chunk 71 optimal weight:    0.8980
   chunk 39 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 73 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 54 optimal weight:    8.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    2.9786

-------------------------------------------------------------------------------
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 = 0.3192 r_free = 0.3192 target = 0.062819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.056316 restraints weight = 41577.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.057059 restraints weight = 28140.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.057606 restraints weight = 20854.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.0871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5507  Z= 0.256
  Angle     :  0.449   5.537   7617  Z= 0.267
  Chirality :  0.040   0.125    957
  Planarity :  0.003   0.038   1037
  Dihedral  :  3.900  16.853    971
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.29), residues: 906
  helix:  2.30 (0.25), residues: 442
  sheet: -0.42 (0.54), residues: 114
  loop : -1.69 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 297 
 HIS   0.005   0.001   HIS R 296 
 PHE   0.016   0.001   PHE R 208 
 TYR   0.012   0.001   TYR A 147 
 ARG   0.002   0.000   ARG B  22 

*********************** 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
  35 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.592 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0752
  time to fit residues: 4.9816
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  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    8.9990
   chunk 35 optimal weight:   10.0000
   chunk 78 optimal weight:    8.9990
   chunk 42 optimal weight:    8.9990
   chunk 93 optimal weight:   20.0000
   chunk 89 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 66 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.061522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.055040 restraints weight = 42200.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.055744 restraints weight = 28463.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.056275 restraints weight = 21111.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5507  Z= 0.345
  Angle     :  0.511   5.518   7617  Z= 0.309
  Chirality :  0.041   0.121    957
  Planarity :  0.003   0.039   1037
  Dihedral  :  4.498  20.361    971
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  9.55 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.29), residues: 906
  helix:  1.85 (0.25), residues: 441
  sheet: -0.56 (0.54), residues: 106
  loop : -2.00 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 297 
 HIS   0.006   0.002   HIS R 172 
 PHE   0.017   0.002   PHE A 340 
 TYR   0.017   0.002   TYR A 147 
 ARG   0.001   0.000   ARG B  22 

*********************** 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
  33 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A  294 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8707 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0752
  time to fit residues: 4.8757
Evaluate side-chains
  32 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 14 optimal weight:    0.0170
   chunk 2 optimal weight:    6.9990
   chunk 15 optimal weight:   10.0000
   chunk 92 optimal weight:    7.9990
   chunk 72 optimal weight:    9.9990
   chunk 48 optimal weight:    0.2980
   chunk 38 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 86 optimal weight:    8.9990
   chunk 10 optimal weight:    8.9990
   overall best weight:    3.6624

-------------------------------------------------------------------------------
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 = 0.3168 r_free = 0.3168 target = 0.061782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.055307 restraints weight = 42621.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.056045 restraints weight = 28727.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.056583 restraints weight = 21272.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5507  Z= 0.309
  Angle     :  0.474   5.418   7617  Z= 0.285
  Chirality :  0.041   0.120    957
  Planarity :  0.003   0.045   1037
  Dihedral  :  4.334  21.066    971
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.29), residues: 906
  helix:  1.86 (0.25), residues: 441
  sheet: -0.81 (0.54), residues: 102
  loop : -1.96 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 297 
 HIS   0.004   0.001   HIS G  44 
 PHE   0.020   0.002   PHE B 278 
 TYR   0.014   0.002   TYR A 147 
 ARG   0.002   0.000   ARG B  22 

*********************** 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
  36 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A  382 ILE cc_start: 0.9302 (mm) cc_final: 0.9038 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0817
  time to fit residues: 5.8033
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  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 86 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 10 optimal weight:    9.9990
   chunk 84 optimal weight:    5.9990
   chunk 88 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   overall best weight:    2.7786

-------------------------------------------------------------------------------
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 = 0.3175 r_free = 0.3175 target = 0.062088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.055619 restraints weight = 41734.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.056341 restraints weight = 28092.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.056867 restraints weight = 20862.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5507  Z= 0.237
  Angle     :  0.440   5.346   7617  Z= 0.262
  Chirality :  0.040   0.118    957
  Planarity :  0.003   0.043   1037
  Dihedral  :  4.094  19.981    971
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.30), residues: 906
  helix:  2.06 (0.26), residues: 441
  sheet: -0.76 (0.54), residues: 101
  loop : -1.88 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  63 
 HIS   0.004   0.001   HIS G  44 
 PHE   0.015   0.002   PHE R 208 
 TYR   0.012   0.001   TYR A 147 
 ARG   0.002   0.000   ARG B  22 

*********************** 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
  33 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.633 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0744
  time to fit residues: 4.8385
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  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 52 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 35 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 57 optimal weight:    7.9990
   chunk 63 optimal weight:    6.9990
   chunk 89 optimal weight:    0.2980
   chunk 27 optimal weight:    6.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3218 r_free = 0.3218 target = 0.063744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.057305 restraints weight = 41104.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.058034 restraints weight = 27929.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.058575 restraints weight = 20619.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5507  Z= 0.108
  Angle     :  0.371   5.331   7617  Z= 0.214
  Chirality :  0.039   0.119    957
  Planarity :  0.003   0.046   1037
  Dihedral  :  3.448  17.940    971
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.30), residues: 906
  helix:  2.48 (0.25), residues: 442
  sheet: -0.58 (0.54), residues: 101
  loop : -1.72 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  63 
 HIS   0.002   0.000   HIS R  93 
 PHE   0.017   0.001   PHE R 208 
 TYR   0.010   0.001   TYR R 219 
 ARG   0.002   0.000   ARG B  22 

*********************** 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  : 0.588 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0729
  time to fit residues: 4.9818
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  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 13 optimal weight:   30.0000
   chunk 60 optimal weight:   10.0000
   chunk 90 optimal weight:    6.9990
   chunk 82 optimal weight:    1.9990
   chunk 35 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 77 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 32 optimal weight:    7.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    2.3386

-------------------------------------------------------------------------------
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 = 0.3193 r_free = 0.3193 target = 0.062765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.056266 restraints weight = 41769.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.057010 restraints weight = 27913.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.057535 restraints weight = 20508.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5507  Z= 0.202
  Angle     :  0.403   5.266   7617  Z= 0.238
  Chirality :  0.040   0.118    957
  Planarity :  0.003   0.044   1037
  Dihedral  :  3.663  18.458    971
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.30), residues: 906
  helix:  2.45 (0.25), residues: 442
  sheet: -0.59 (0.55), residues: 101
  loop : -1.80 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 297 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.020   0.001   PHE R 208 
 TYR   0.012   0.001   TYR A 360 
 ARG   0.001   0.000   ARG B  22 

*********************** 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  : 0.632 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0713
  time to fit residues: 4.8262
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  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 59 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 37 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 87 optimal weight:    0.0980
   overall best weight:    1.1782

-------------------------------------------------------------------------------
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 = 0.3218 r_free = 0.3218 target = 0.063685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.057212 restraints weight = 41367.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.057962 restraints weight = 28046.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.058503 restraints weight = 20553.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
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      :  0.002   0.022   5507  Z= 0.114
  Angle     :  0.363   5.319   7617  Z= 0.209
  Chirality :  0.039   0.119    957
  Planarity :  0.003   0.044   1037
  Dihedral  :  3.339  16.890    971
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.30), residues: 906
  helix:  2.67 (0.25), residues: 442
  sheet: -0.63 (0.54), residues: 101
  loop : -1.72 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 297 
 HIS   0.002   0.001   HIS B  54 
 PHE   0.020   0.001   PHE R 208 
 TYR   0.010   0.001   TYR R 219 
 ARG   0.002   0.000   ARG B  22 

*********************** 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
  33 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.681 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0809
  time to fit residues: 5.2381
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  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 46 optimal weight:    9.9990
   chunk 90 optimal weight:    0.9980
   chunk 80 optimal weight:    0.0770
   chunk 51 optimal weight:   20.0000
   chunk 35 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 18 optimal weight:    5.9990
   chunk 43 optimal weight:   20.0000
   overall best weight:    2.1942

-------------------------------------------------------------------------------
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 = 0.3199 r_free = 0.3199 target = 0.063003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.056523 restraints weight = 41345.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.057261 restraints weight = 27860.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.057787 restraints weight = 20587.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5507  Z= 0.186
  Angle     :  0.392   5.304   7617  Z= 0.230
  Chirality :  0.039   0.119    957
  Planarity :  0.003   0.043   1037
  Dihedral  :  3.527  17.349    971
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.29), residues: 906
  helix:  2.53 (0.25), residues: 448
  sheet: -0.70 (0.54), residues: 101
  loop : -1.80 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 297 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.020   0.001   PHE R 208 
 TYR   0.011   0.001   TYR A 360 
 ARG   0.001   0.000   ARG B  22 

*********************** 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
  33 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.598 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0703
  time to fit residues: 4.6412
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  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 21 optimal weight:   10.0000
   chunk 7 optimal weight:   20.0000
   chunk 54 optimal weight:    6.9990
   chunk 10 optimal weight:   40.0000
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 86 optimal weight:    7.9990
   chunk 89 optimal weight:    0.0870
   chunk 13 optimal weight:   30.0000
   overall best weight:    3.9764

-------------------------------------------------------------------------------
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 = 0.3160 r_free = 0.3160 target = 0.061567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.055120 restraints weight = 41952.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.055836 restraints weight = 28432.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.056365 restraints weight = 21025.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5507  Z= 0.322
  Angle     :  0.495   5.396   7617  Z= 0.300
  Chirality :  0.041   0.124    957
  Planarity :  0.003   0.042   1037
  Dihedral  :  4.391  20.022    971
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.29), residues: 906
  helix:  2.06 (0.25), residues: 435
  sheet: -1.15 (0.54), residues: 106
  loop : -1.80 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 297 
 HIS   0.005   0.002   HIS G  44 
 PHE   0.022   0.002   PHE R 133 
 TYR   0.019   0.002   TYR R 209 
 ARG   0.001   0.000   ARG B  22 

********************** 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
  34 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.628 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0736
  time to fit residues: 4.8996
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  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9980
   chunk 30 optimal weight:    9.9990
   chunk 75 optimal weight:    0.9980
   chunk 27 optimal weight:    7.9990
   chunk 5 optimal weight:   20.0000
   chunk 35 optimal weight:    1.9990
   chunk 50 optimal weight:    9.9990
   chunk 26 optimal weight:    0.8980
   chunk 92 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   overall best weight:    2.1784

-------------------------------------------------------------------------------
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 = 0.3190 r_free = 0.3190 target = 0.062603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.056086 restraints weight = 42078.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.056811 restraints weight = 28409.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.057332 restraints weight = 21000.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5507  Z= 0.187
  Angle     :  0.409   5.255   7617  Z= 0.240
  Chirality :  0.040   0.117    957
  Planarity :  0.003   0.043   1037
  Dihedral  :  3.848  18.387    971
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.23
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.30), residues: 906
  helix:  2.35 (0.25), residues: 435
  sheet: -1.10 (0.53), residues: 106
  loop : -1.65 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 297 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.020   0.002   PHE R 208 
 TYR   0.012   0.001   TYR A 147 
 ARG   0.002   0.000   ARG B  22 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1468.29 seconds
wall clock time: 26 minutes 8.97 seconds (1568.97 seconds total)