Starting phenix.real_space_refine
on Sat Jun  7 12:40:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8flq_29283/06_2025/8flq_29283.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8flq_29283/06_2025/8flq_29283.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8flq_29283/06_2025/8flq_29283.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8flq_29283/06_2025/8flq_29283.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8flq_29283/06_2025/8flq_29283.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8flq_29283/06_2025/8flq_29283.cif"
  }
  resolution = 2.55
  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=   0.070
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      58      5.16       5
     C    5709      2.51       5
     N    1569      2.21       5
     O    1656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8992
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1906
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2568
          Classifications: {'peptide': 337}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 424
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5
    Chain: "N"
      Number of atoms: 953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 953
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "P"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 269
          Classifications: {'peptide': 32}
          Link IDs: {'TRANS': 31}
    Chain: "R"
      Number of atoms: 2858
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2858
          Classifications: {'peptide': 363}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 11, 'TRANS': 351}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 133
          Unresolved non-hydrogen angles: 164
          Unresolved non-hydrogen dihedrals: 111
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 80
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "P"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "R"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 11
          Classifications: {'water': 11}
          Link IDs: {None: 10}
  Time building chain proxies: 5.85, per 1000 atoms: 0.65
  Number of scatterers: 8992
  At special positions: 0
  Unit cell: (72.8, 96.2, 173.55, 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      58     16.00
     O    1656      8.00
     N    1569      7.00
     C    5709      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  48 " - pdb=" SG  CYS R 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 131 " - pdb=" SG  CYS R 170 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 281 " - pdb=" SG  CYS R 351 " 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: 2.39
  Conformation dependent library (CDL) restraints added in 977.4 milliseconds
  

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2152

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      43.9% alpha, 19.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 39
      removed outlier: 3.567A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 63
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.504A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.592A  pdb=" N   ALA A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.257A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 4.120A  pdb=" N   ARG A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.851A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 391
      removed outlier: 4.517A  pdb=" N   ARG A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 25
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'P' and resid 2 through 32
    Processing helix  chain 'R' and resid 33 through 53
    Processing helix  chain 'R' and resid 167 through 172
      removed outlier: 4.053A  pdb=" N   LYS R 172 " --> pdb=" O   GLU R 169 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 212
      removed outlier: 4.482A  pdb=" N   ARG R 181 " --> pdb=" O   GLU R 177 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 246
      removed outlier: 3.588A  pdb=" N   SER R 246 " --> pdb=" O   ALA R 242 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 278 through 312
      removed outlier: 3.529A  pdb=" N   ARG R 282 " --> pdb=" O   TYR R 278 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ALA R 284 " --> pdb=" O   GLY R 280 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 347
      removed outlier: 3.538A  pdb=" N   TYR R 320 " --> pdb=" O   SER R 316 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   TRP R 322 " --> pdb=" O   LYS R 318 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   GLY R 323 " --> pdb=" O   LYS R 319 " (cutoff:3.500A)
      Proline residue:  R 332  - end of helix
      removed outlier: 3.516A  pdb=" N   PHE R 335 " --> pdb=" O   LEU R 331 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 356 through 359
    Processing helix  chain 'R' and resid 360 through 392
      Proline residue:  R 366  - end of helix
    Processing helix  chain 'R' and resid 400 through 418
      Proline residue:  R 415  - end of helix
    Processing helix  chain 'R' and resid 419 through 423
    Processing helix  chain 'R' and resid 434 through 460
      removed outlier: 4.385A  pdb=" N   GLY R 452 " --> pdb=" O   ASN R 448 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   PHE R 453 " --> pdb=" O   SER R 449 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 463 through 479
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.345A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.438A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.584A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.947A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.549A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.292A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.235A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.551A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.093A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.142A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.562A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.674A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.619A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112
      removed outlier: 3.664A  pdb=" N   GLU R 111 " --> pdb=" O   TRP R 118 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130

    494 hydrogen bonds defined for protein.
    1407 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.58

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2941
        1.34 -     1.46: 2250
        1.46 -     1.58: 3904
        1.58 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 9177
  Sorted by residual:
  bond pdb=" N   VAL B 187 "
       pdb=" CA  VAL B 187 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.17e-02 7.31e+03 7.88e+00
  bond pdb=" N   SER B 160 "
       pdb=" CA  SER B 160 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.23e-02 6.61e+03 6.91e+00
  bond pdb=" N   CYS B 166 "
       pdb=" CA  CYS B 166 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.23e-02 6.61e+03 6.89e+00
  bond pdb=" N   THR B 165 "
       pdb=" CA  THR B 165 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.29e-02 6.01e+03 6.62e+00
  bond pdb=" CA  SER B 316 "
       pdb=" CB  SER B 316 "
    ideal  model  delta    sigma   weight residual
    1.531  1.491  0.040 1.56e-02 4.11e+03 6.62e+00
  ... (remaining 9172 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 12017
        1.37 -     2.75: 349
        2.75 -     4.12: 65
        4.12 -     5.49: 12
        5.49 -     6.87: 4
  Bond angle restraints: 12447
  Sorted by residual:
  angle pdb=" N   GLY B 162 "
        pdb=" CA  GLY B 162 "
        pdb=" C   GLY B 162 "
      ideal   model   delta    sigma   weight residual
     114.67  109.69    4.98 1.10e+00 8.26e-01 2.05e+01
  angle pdb=" N   ASP B 163 "
        pdb=" CA  ASP B 163 "
        pdb=" C   ASP B 163 "
      ideal   model   delta    sigma   weight residual
     113.19  108.03    5.16 1.19e+00 7.06e-01 1.88e+01
  angle pdb=" C   ILE R 190 "
        pdb=" N   TYR R 191 "
        pdb=" CA  TYR R 191 "
      ideal   model   delta    sigma   weight residual
     121.14  114.27    6.87 1.75e+00 3.27e-01 1.54e+01
  angle pdb=" N   TYR B  59 "
        pdb=" CA  TYR B  59 "
        pdb=" C   TYR B  59 "
      ideal   model   delta    sigma   weight residual
     113.41  109.21    4.20 1.22e+00 6.72e-01 1.19e+01
  angle pdb=" CA  TYR R 191 "
        pdb=" CB  TYR R 191 "
        pdb=" CG  TYR R 191 "
      ideal   model   delta    sigma   weight residual
     113.90  120.00   -6.10 1.80e+00 3.09e-01 1.15e+01
  ... (remaining 12442 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 4907
       17.66 -    35.32: 415
       35.32 -    52.98: 64
       52.98 -    70.63: 16
       70.63 -    88.29: 9
  Dihedral angle restraints: 5411
    sinusoidal: 2081
      harmonic: 3330
  Sorted by residual:
  dihedral pdb=" CB  CYS R 281 "
           pdb=" SG  CYS R 281 "
           pdb=" SG  CYS R 351 "
           pdb=" CB  CYS R 351 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.52  -50.52     1      1.00e+01 1.00e-02 3.50e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.25   24.75     0      5.00e+00 4.00e-02 2.45e+01
  dihedral pdb=" CA  LEU A 291 "
           pdb=" C   LEU A 291 "
           pdb=" N   ASN A 292 "
           pdb=" CA  ASN A 292 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.28  -22.72     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 5408 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 970
       0.039 -    0.077: 308
       0.077 -    0.116: 87
       0.116 -    0.155: 18
       0.155 -    0.193: 3
  Chirality restraints: 1386
  Sorted by residual:
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.33e-01
  chirality pdb=" CB  ILE R 190 "
            pdb=" CA  ILE R 190 "
            pdb=" CG1 ILE R 190 "
            pdb=" CG2 ILE R 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.18e-01
  chirality pdb=" CA  VAL B 187 "
            pdb=" N   VAL B 187 "
            pdb=" C   VAL B 187 "
            pdb=" CB  VAL B 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.96e-01
  ... (remaining 1383 not shown)

  Planarity restraints: 1588
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 376 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.09e+00
        pdb=" C   ILE R 376 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ILE R 376 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU R 377 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 378 "   -0.009 2.00e-02 2.50e+03   1.75e-02 3.06e+00
        pdb=" C   PHE R 378 "    0.030 2.00e-02 2.50e+03
        pdb=" O   PHE R 378 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ILE R 379 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 377 "   -0.009 2.00e-02 2.50e+03   1.71e-02 2.92e+00
        pdb=" C   LEU R 377 "    0.030 2.00e-02 2.50e+03
        pdb=" O   LEU R 377 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   PHE R 378 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1585 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 926
        2.75 -     3.29: 9083
        3.29 -     3.82: 16195
        3.82 -     4.36: 19609
        4.36 -     4.90: 32721
  Nonbonded interactions: 78534
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OD1 ASP A 274 "
            pdb=" ND2 ASN A 278 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" OE2 GLU A 330 "
            pdb=" OG1 THR A 335 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   ARG N  98 "
            pdb=" OH  TYR N 115 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OE1 GLU R 302 "
            pdb=" O   HOH R 701 "
     model   vdw
     2.265 3.040
  ... (remaining 78529 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.620
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:12.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6672
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9183  Z= 0.198
  Angle     :  0.569   6.865  12459  Z= 0.353
  Chirality :  0.042   0.193   1386
  Planarity :  0.004   0.036   1588
  Dihedral  : 13.874  88.292   3241
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.53 %
    Favored  : 99.25 %
  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:  1.35 (0.25), residues: 1124
  helix:  2.39 (0.24), residues: 443
  sheet: -0.26 (0.33), residues: 214
  loop :  0.08 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  82 
 HIS   0.009   0.001   HIS A 357 
 PHE   0.021   0.001   PHE R 335 
 TYR   0.013   0.001   TYR A 358 
 ARG   0.007   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13542 (  494)
  hydrogen bonds       : angle       6.06927 ( 1407)
  SS BOND              : bond        0.00095 (    6)
  SS BOND              : angle       0.92810 (   12)
  covalent geometry    : bond        0.00327 ( 9177)
  covalent geometry    : angle       0.56880 (12447)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 1.016 
Fit side-chains
REVERT: R   32 MET cc_start: 0.4510 (ptt) cc_final: 0.4234 (tpp)
  outliers start: 2
  outliers final: 2
  residues processed: 128
  average time/residue: 1.3757
  time to fit residues: 187.6567
Evaluate side-chains
  110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 108
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  317 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 84 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 57 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   chunk 87 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 65 optimal weight:    0.2980
   chunk 101 optimal weight:    0.0060
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
N  39 GLN
N 123 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.194969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.148508 restraints weight = 9846.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 2.32
r_work: 0.3588 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.0949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9183  Z= 0.121
  Angle     :  0.486   5.794  12459  Z= 0.271
  Chirality :  0.041   0.175   1386
  Planarity :  0.004   0.034   1588
  Dihedral  :  4.393  23.956   1250
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  7.46 %
    Favored  : 91.79 %
  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:  1.70 (0.26), residues: 1124
  helix:  2.91 (0.24), residues: 438
  sheet: -0.33 (0.31), residues: 231
  loop :  0.23 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 339 
 HIS   0.010   0.001   HIS A 357 
 PHE   0.022   0.001   PHE R 335 
 TYR   0.025   0.001   TYR R 191 
 ARG   0.007   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04297 (  494)
  hydrogen bonds       : angle       4.68907 ( 1407)
  SS BOND              : bond        0.00118 (    6)
  SS BOND              : angle       0.71900 (   12)
  covalent geometry    : bond        0.00245 ( 9177)
  covalent geometry    : angle       0.48535 (12447)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 1.047 
Fit side-chains
REVERT: B   66 ASP cc_start: 0.7107 (p0) cc_final: 0.6358 (m-30)
REVERT: B   76 ASP cc_start: 0.8533 (p0) cc_final: 0.8326 (p0)
REVERT: B  255 LEU cc_start: 0.8205 (mp) cc_final: 0.7953 (mt)
REVERT: B  303 ASP cc_start: 0.7832 (m-30) cc_final: 0.7492 (m-30)
REVERT: R   32 MET cc_start: 0.6561 (ptt) cc_final: 0.4439 (tpp)
REVERT: R  221 TYR cc_start: 0.7552 (m-10) cc_final: 0.6549 (t80)
  outliers start: 7
  outliers final: 5
  residues processed: 120
  average time/residue: 1.1648
  time to fit residues: 150.7033
Evaluate side-chains
  117 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 112
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain R residue  384 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 88 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
N  84 ASN
R 448 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.194164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.147175 restraints weight = 10005.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3720 rms_B_bonded: 2.32
r_work: 0.3571 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3451 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9183  Z= 0.118
  Angle     :  0.476   6.179  12459  Z= 0.263
  Chirality :  0.041   0.185   1386
  Planarity :  0.003   0.036   1588
  Dihedral  :  4.338  22.836   1249
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 10.23 %
    Favored  : 88.91 %
  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:  1.72 (0.26), residues: 1124
  helix:  2.98 (0.24), residues: 437
  sheet: -0.38 (0.31), residues: 236
  loop :  0.24 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 339 
 HIS   0.009   0.001   HIS A 357 
 PHE   0.019   0.001   PHE R 335 
 TYR   0.022   0.001   TYR R 191 
 ARG   0.007   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04050 (  494)
  hydrogen bonds       : angle       4.48209 ( 1407)
  SS BOND              : bond        0.00114 (    6)
  SS BOND              : angle       1.06131 (   12)
  covalent geometry    : bond        0.00247 ( 9177)
  covalent geometry    : angle       0.47479 (12447)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 1.015 
Fit side-chains
REVERT: B   66 ASP cc_start: 0.7196 (p0) cc_final: 0.6438 (m-30)
REVERT: B   76 ASP cc_start: 0.8602 (p0) cc_final: 0.8346 (p0)
REVERT: B  303 ASP cc_start: 0.7826 (m-30) cc_final: 0.7479 (m-30)
REVERT: R   32 MET cc_start: 0.6523 (ptt) cc_final: 0.4548 (tpp)
REVERT: R  221 TYR cc_start: 0.7650 (m-10) cc_final: 0.6674 (t80)
REVERT: R  414 MET cc_start: 0.8353 (mtp) cc_final: 0.8124 (mtt)
  outliers start: 8
  outliers final: 4
  residues processed: 113
  average time/residue: 1.4963
  time to fit residues: 182.4308
Evaluate side-chains
  109 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain R residue  384 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 57 optimal weight:    8.9990
   chunk 101 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 107 optimal weight:    0.0870
   chunk 78 optimal weight:    6.9990
   overall best weight:    0.7964

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

Flipped N/Q/H residues before XYZ refinement:
N 123 GLN
R 448 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.194110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.147124 restraints weight = 9933.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3720 rms_B_bonded: 2.38
r_work: 0.3573 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3451 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9183  Z= 0.118
  Angle     :  0.467   6.272  12459  Z= 0.258
  Chirality :  0.040   0.201   1386
  Planarity :  0.003   0.036   1588
  Dihedral  :  4.321  24.684   1249
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 10.66 %
    Favored  : 88.27 %
  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:  1.73 (0.26), residues: 1124
  helix:  2.93 (0.24), residues: 444
  sheet: -0.38 (0.31), residues: 236
  loop :  0.24 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 339 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.018   0.001   PHE R 335 
 TYR   0.023   0.001   TYR R 191 
 ARG   0.006   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03934 (  494)
  hydrogen bonds       : angle       4.39955 ( 1407)
  SS BOND              : bond        0.00089 (    6)
  SS BOND              : angle       1.02908 (   12)
  covalent geometry    : bond        0.00250 ( 9177)
  covalent geometry    : angle       0.46573 (12447)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.922 
Fit side-chains
REVERT: B   66 ASP cc_start: 0.7200 (p0) cc_final: 0.6459 (m-30)
REVERT: B   76 ASP cc_start: 0.8626 (p0) cc_final: 0.8353 (p0)
REVERT: B  303 ASP cc_start: 0.7822 (m-30) cc_final: 0.7485 (m-30)
REVERT: R   32 MET cc_start: 0.6499 (ptt) cc_final: 0.4607 (tpp)
REVERT: R  221 TYR cc_start: 0.7687 (m-10) cc_final: 0.6752 (t80)
REVERT: R  463 ASN cc_start: 0.8441 (t0) cc_final: 0.8017 (t0)
  outliers start: 10
  outliers final: 5
  residues processed: 118
  average time/residue: 1.3628
  time to fit residues: 173.5541
Evaluate side-chains
  114 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 109
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  384 VAL
Chi-restraints excluded: chain R residue  471 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 57 optimal weight:    8.9990
   chunk 83 optimal weight:   10.0000
   chunk 107 optimal weight:    8.9990
   chunk 47 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   chunk 99 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
N  39 GLN
N  53 GLN
N  82 GLN
R 448 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.185708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.136444 restraints weight = 9859.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 2.28
r_work: 0.3449 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.059   9183  Z= 0.335
  Angle     :  0.667   6.710  12459  Z= 0.364
  Chirality :  0.049   0.206   1386
  Planarity :  0.005   0.047   1588
  Dihedral  :  5.182  26.532   1247
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.51 %
    Favored  : 86.89 %
  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:  1.13 (0.25), residues: 1124
  helix:  2.24 (0.23), residues: 444
  sheet: -0.53 (0.31), residues: 233
  loop :  0.04 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP A 234 
 HIS   0.020   0.002   HIS A 357 
 PHE   0.027   0.002   PHE R 335 
 TYR   0.021   0.003   TYR A 358 
 ARG   0.005   0.001   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05323 (  494)
  hydrogen bonds       : angle       4.93380 ( 1407)
  SS BOND              : bond        0.00097 (    6)
  SS BOND              : angle       1.44939 (   12)
  covalent geometry    : bond        0.00771 ( 9177)
  covalent geometry    : angle       0.66575 (12447)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.972 
Fit side-chains
REVERT: B   66 ASP cc_start: 0.7333 (p0) cc_final: 0.6771 (m-30)
REVERT: B  263 THR cc_start: 0.8069 (m) cc_final: 0.7807 (m)
REVERT: B  303 ASP cc_start: 0.7934 (m-30) cc_final: 0.7696 (m-30)
REVERT: N  123 GLN cc_start: 0.7922 (tp-100) cc_final: 0.7721 (tp40)
REVERT: R   32 MET cc_start: 0.6674 (ptt) cc_final: 0.4688 (tpp)
REVERT: R  221 TYR cc_start: 0.7789 (m-10) cc_final: 0.6818 (t80)
  outliers start: 15
  outliers final: 6
  residues processed: 114
  average time/residue: 1.2640
  time to fit residues: 154.5764
Evaluate side-chains
  109 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  191 TYR
Chi-restraints excluded: chain R residue  384 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 92 optimal weight:    0.3980
   chunk 83 optimal weight:    0.0060
   chunk 21 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
N  39 GLN
R 380 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.193023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.146061 restraints weight = 9872.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 2.46
r_work: 0.3563 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3445 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9183  Z= 0.110
  Angle     :  0.482   7.863  12459  Z= 0.266
  Chirality :  0.040   0.219   1386
  Planarity :  0.004   0.039   1588
  Dihedral  :  4.474  23.843   1247
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 13.11 %
    Favored  : 86.03 %
  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:  1.51 (0.25), residues: 1124
  helix:  2.79 (0.24), residues: 437
  sheet: -0.51 (0.30), residues: 236
  loop :  0.15 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 211 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.022   0.001   PHE R 335 
 TYR   0.023   0.001   TYR R 191 
 ARG   0.009   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03908 (  494)
  hydrogen bonds       : angle       4.47926 ( 1407)
  SS BOND              : bond        0.00073 (    6)
  SS BOND              : angle       0.80522 (   12)
  covalent geometry    : bond        0.00220 ( 9177)
  covalent geometry    : angle       0.48204 (12447)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.892 
Fit side-chains
REVERT: B   76 ASP cc_start: 0.8490 (p0) cc_final: 0.8279 (p0)
REVERT: B  303 ASP cc_start: 0.7859 (m-30) cc_final: 0.7575 (m-30)
REVERT: R   32 MET cc_start: 0.6599 (ptt) cc_final: 0.4823 (tpp)
REVERT: R  221 TYR cc_start: 0.7636 (m-10) cc_final: 0.6680 (t80)
  outliers start: 8
  outliers final: 3
  residues processed: 115
  average time/residue: 1.1548
  time to fit residues: 142.5243
Evaluate side-chains
  108 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 105
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain R residue  191 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 74 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 81 optimal weight:   20.0000
   chunk 63 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 98 optimal weight:    0.4980
   chunk 76 optimal weight:    1.9990
   chunk 80 optimal weight:   20.0000
   chunk 48 optimal weight:    0.7980
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
N 123 GLN
R 448 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.191631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.144211 restraints weight = 9999.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 2.51
r_work: 0.3540 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3418 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9183  Z= 0.138
  Angle     :  0.502   6.693  12459  Z= 0.276
  Chirality :  0.041   0.232   1386
  Planarity :  0.004   0.039   1588
  Dihedral  :  4.478  23.299   1247
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 13.33 %
    Favored  : 85.61 %
  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:  1.51 (0.26), residues: 1124
  helix:  2.75 (0.24), residues: 444
  sheet: -0.56 (0.30), residues: 239
  loop :  0.18 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 234 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.021   0.001   PHE R 335 
 TYR   0.022   0.001   TYR R 191 
 ARG   0.008   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04069 (  494)
  hydrogen bonds       : angle       4.44558 ( 1407)
  SS BOND              : bond        0.00069 (    6)
  SS BOND              : angle       0.86972 (   12)
  covalent geometry    : bond        0.00299 ( 9177)
  covalent geometry    : angle       0.50117 (12447)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 1.184 
Fit side-chains
REVERT: A  297 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6399 (tp)
REVERT: B   76 ASP cc_start: 0.8567 (p0) cc_final: 0.8328 (p0)
REVERT: B  303 ASP cc_start: 0.7934 (m-30) cc_final: 0.7673 (m-30)
REVERT: R   32 MET cc_start: 0.6611 (ptt) cc_final: 0.4801 (tpt)
REVERT: R  221 TYR cc_start: 0.7661 (m-10) cc_final: 0.6697 (t80)
  outliers start: 10
  outliers final: 3
  residues processed: 111
  average time/residue: 1.6803
  time to fit residues: 199.4435
Evaluate side-chains
  104 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  191 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 7 optimal weight:    0.2980
   chunk 91 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 103 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0670
   chunk 108 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0970
   chunk 69 optimal weight:    5.9990
   chunk 94 optimal weight:    0.5980
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
R 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.195040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.148705 restraints weight = 10067.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 2.43
r_work: 0.3592 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3470 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9183  Z= 0.100
  Angle     :  0.463   6.295  12459  Z= 0.255
  Chirality :  0.040   0.240   1386
  Planarity :  0.003   0.038   1588
  Dihedral  :  4.208  22.654   1247
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 13.97 %
    Favored  : 85.18 %
  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:  1.72 (0.26), residues: 1124
  helix:  2.97 (0.24), residues: 438
  sheet: -0.38 (0.31), residues: 232
  loop :  0.21 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 298 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.019   0.001   PHE R 335 
 TYR   0.023   0.001   TYR R 191 
 ARG   0.007   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03709 (  494)
  hydrogen bonds       : angle       4.27262 ( 1407)
  SS BOND              : bond        0.00090 (    6)
  SS BOND              : angle       0.77293 (   12)
  covalent geometry    : bond        0.00204 ( 9177)
  covalent geometry    : angle       0.46221 (12447)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.899 
Fit side-chains
REVERT: A  297 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6300 (tp)
REVERT: B   46 ARG cc_start: 0.8653 (mtt-85) cc_final: 0.8374 (mtm-85)
REVERT: B   59 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.8673 (t80)
REVERT: B   76 ASP cc_start: 0.8508 (p0) cc_final: 0.8283 (p0)
REVERT: B  303 ASP cc_start: 0.7941 (m-30) cc_final: 0.7658 (m-30)
REVERT: R   32 MET cc_start: 0.6512 (ptt) cc_final: 0.4739 (tpt)
REVERT: R  221 TYR cc_start: 0.7645 (m-10) cc_final: 0.6744 (t80)
  outliers start: 8
  outliers final: 2
  residues processed: 115
  average time/residue: 1.0984
  time to fit residues: 136.1533
Evaluate side-chains
  107 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  191 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 7 optimal weight:    0.0370
   chunk 86 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 81 optimal weight:    8.9990
   chunk 48 optimal weight:    0.5980
   chunk 19 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.8660

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

Flipped N/Q/H residues before XYZ refinement:
N 123 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.193351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.146253 restraints weight = 9903.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 2.43
r_work: 0.3564 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9183  Z= 0.123
  Angle     :  0.481   6.286  12459  Z= 0.264
  Chirality :  0.041   0.240   1386
  Planarity :  0.003   0.037   1588
  Dihedral  :  4.290  22.496   1247
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 15.35 %
    Favored  : 84.12 %
  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:  1.68 (0.26), residues: 1124
  helix:  2.95 (0.24), residues: 438
  sheet: -0.44 (0.31), residues: 236
  loop :  0.22 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 234 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.018   0.001   PHE R 335 
 TYR   0.023   0.001   TYR R 191 
 ARG   0.006   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03876 (  494)
  hydrogen bonds       : angle       4.32531 ( 1407)
  SS BOND              : bond        0.00059 (    6)
  SS BOND              : angle       0.79424 (   12)
  covalent geometry    : bond        0.00266 ( 9177)
  covalent geometry    : angle       0.48100 (12447)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 1.024 
Fit side-chains
REVERT: A  297 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6340 (tp)
REVERT: B   46 ARG cc_start: 0.8686 (mtt-85) cc_final: 0.8293 (mpt90)
REVERT: B   76 ASP cc_start: 0.8571 (p0) cc_final: 0.8329 (p0)
REVERT: B  303 ASP cc_start: 0.7936 (m-30) cc_final: 0.7676 (m-30)
REVERT: N   39 GLN cc_start: 0.7713 (tt0) cc_final: 0.7459 (tp40)
REVERT: R   32 MET cc_start: 0.6549 (ptt) cc_final: 0.4765 (tpt)
REVERT: R  221 TYR cc_start: 0.7679 (m-10) cc_final: 0.6758 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 109
  average time/residue: 1.1473
  time to fit residues: 134.6401
Evaluate side-chains
  108 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  191 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 43 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 40 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
R 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.190673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.142653 restraints weight = 9901.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 2.49
r_work: 0.3518 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9183  Z= 0.166
  Angle     :  0.523   6.425  12459  Z= 0.286
  Chirality :  0.042   0.240   1386
  Planarity :  0.004   0.041   1588
  Dihedral  :  4.548  22.924   1247
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 15.35 %
    Favored  : 84.01 %
  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:  1.52 (0.26), residues: 1124
  helix:  2.76 (0.24), residues: 444
  sheet: -0.58 (0.30), residues: 241
  loop :  0.21 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 234 
 HIS   0.009   0.001   HIS A 357 
 PHE   0.021   0.002   PHE R 212 
 TYR   0.022   0.002   TYR R 191 
 ARG   0.006   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04212 (  494)
  hydrogen bonds       : angle       4.46192 ( 1407)
  SS BOND              : bond        0.00061 (    6)
  SS BOND              : angle       0.98825 (   12)
  covalent geometry    : bond        0.00369 ( 9177)
  covalent geometry    : angle       0.52238 (12447)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A  297 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6312 (tp)
REVERT: B   46 ARG cc_start: 0.8683 (mtt-85) cc_final: 0.8296 (mpt90)
REVERT: B   76 ASP cc_start: 0.8622 (p0) cc_final: 0.8358 (p0)
REVERT: B  303 ASP cc_start: 0.7954 (m-30) cc_final: 0.7708 (m-30)
REVERT: R   32 MET cc_start: 0.6562 (ptt) cc_final: 0.4776 (tpt)
REVERT: R  221 TYR cc_start: 0.7685 (m-10) cc_final: 0.6755 (t80)
  outliers start: 6
  outliers final: 3
  residues processed: 105
  average time/residue: 1.1481
  time to fit residues: 129.7160
Evaluate side-chains
  105 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  191 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 7 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   chunk 102 optimal weight:    0.7980
   chunk 93 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4210 r_free = 0.4210 target = 0.193571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.146421 restraints weight = 9973.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 2.43
r_work: 0.3569 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3450 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9183  Z= 0.114
  Angle     :  0.476   6.332  12459  Z= 0.262
  Chirality :  0.040   0.240   1386
  Planarity :  0.003   0.038   1588
  Dihedral  :  4.289  22.457   1247
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 15.25 %
    Favored  : 83.90 %
  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:  1.65 (0.25), residues: 1124
  helix:  2.93 (0.24), residues: 438
  sheet: -0.46 (0.31), residues: 236
  loop :  0.19 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 298 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.019   0.001   PHE R 335 
 TYR   0.023   0.001   TYR R 191 
 ARG   0.008   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03825 (  494)
  hydrogen bonds       : angle       4.34508 ( 1407)
  SS BOND              : bond        0.00051 (    6)
  SS BOND              : angle       0.81721 (   12)
  covalent geometry    : bond        0.00240 ( 9177)
  covalent geometry    : angle       0.47529 (12447)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8819.07 seconds
wall clock time: 153 minutes 39.68 seconds (9219.68 seconds total)