Starting phenix.real_space_refine
on Tue Sep 24 13:41:55 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vvh_43559/09_2024/8vvh_43559.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vvh_43559/09_2024/8vvh_43559.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vvh_43559/09_2024/8vvh_43559.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vvh_43559/09_2024/8vvh_43559.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vvh_43559/09_2024/8vvh_43559.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vvh_43559/09_2024/8vvh_43559.cif"
  }
  resolution = 3.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1632 atoms to isotropic.
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      27      5.16       5
     C    4368      2.51       5
     N    1180      2.21       5
     O    1302      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 6877
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2684
          Classifications: {'peptide': 364}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PTRANS': 17, 'TRANS': 346}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 185
          Unresolved non-hydrogen angles: 228
          Unresolved non-hydrogen dihedrals: 155
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 134
    Chain: "B"
      Number of atoms: 2624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 2624
          Classifications: {'peptide': 354}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'PTRANS': 13, 'TRANS': 340}
          Unresolved non-hydrogen bonds: 201
          Unresolved non-hydrogen angles: 249
          Unresolved non-hydrogen dihedrals: 172
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 10, 'TYR:plan': 3, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 140
    Chain: "H"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 833
          Classifications: {'peptide': 115}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 108}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "L"
      Number of atoms: 736
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 108, 726
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 6, 'TRANS': 101}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 109
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 48
      Conformer: "B"
        Number of residues, atoms: 108, 726
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 6, 'TRANS': 101}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 109
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 48
          bond proxies already assigned to first conformer: 728
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS L   8 " occ=0.82
      ... (18 atoms not shown)
      pdb=" NE2BHIS L   8 " occ=0.18
  Time building chain proxies: 6.00, per 1000 atoms: 0.87
  Number of scatterers: 6877
  At special positions: 0
  Unit cell: (109.568, 123.264, 83.888, 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      27     16.00
     O    1302      8.00
     N    1180      7.00
     C    4368      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  79 " - pdb=" SG  CYS A 308 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  86 " - pdb=" SG  CYS B 321 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  91 " 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: 1.60
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1754

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 12 sheets defined
      28.3% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 51
      removed outlier: 3.507A  pdb=" N   LYS A  51 " --> pdb=" O   ASN A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 86
      removed outlier: 3.627A  pdb=" N   SER A  85 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 115
      removed outlier: 3.695A  pdb=" N   SER A 108 " --> pdb=" O   PRO A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 130
      removed outlier: 3.561A  pdb=" N   ASP A 130 " --> pdb=" O   ILE A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 147
      removed outlier: 3.925A  pdb=" N   GLN A 147 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 159
      removed outlier: 3.924A  pdb=" N   PHE A 152 " --> pdb=" O   SER A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 185
    Processing helix  chain 'A' and resid 204 through 212
    Processing helix  chain 'A' and resid 224 through 238
      removed outlier: 4.471A  pdb=" N   THR A 230 " --> pdb=" O   ASP A 226 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   VAL A 231 " --> pdb=" O   ASP A 227 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   MET A 237 " --> pdb=" O   ARG A 233 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU A 238 " --> pdb=" O   ALA A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 296
      removed outlier: 4.068A  pdb=" N   HIS A 280 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU A 296 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 327
      removed outlier: 3.700A  pdb=" N   SER A 327 " --> pdb=" O   ARG A 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 92
      removed outlier: 4.059A  pdb=" N   ARG B  92 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 119
    Processing helix  chain 'B' and resid 130 through 132
      No H-bonds generated for 'chain 'B' and resid 130 through 132'
    Processing helix  chain 'B' and resid 150 through 164
      removed outlier: 3.587A  pdb=" N   ALA B 154 " --> pdb=" O   ILE B 150 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   TYR B 164 " --> pdb=" O   ILE B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 192
      removed outlier: 3.761A  pdb=" N   ASN B 192 " --> pdb=" O   SER B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 223
      removed outlier: 4.015A  pdb=" N   ILE B 216 " --> pdb=" O   GLY B 212 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   LEU B 223 " --> pdb=" O   GLN B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 248
      removed outlier: 3.857A  pdb=" N   TYR B 239 " --> pdb=" O   GLU B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 264
      removed outlier: 3.908A  pdb=" N   ALA B 263 " --> pdb=" O   PRO B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 312
    Processing helix  chain 'B' and resid 333 through 339
    Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65
      removed outlier: 6.357A  pdb=" N   ILE A  90 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197
      removed outlier: 6.854A  pdb=" N   LEU A 165 " --> pdb=" O   LEU A 195 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   PHE A 197 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   VAL A 167 " --> pdb=" O   PHE A 197 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   SER A 168 " --> pdb=" O   SER A 222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271
      removed outlier: 6.095A  pdb=" N   ASN A 355 " --> pdb=" O   GLN A 363 " (cutoff:3.500A)
      removed outlier: 5.466A  pdb=" N   GLN A 363 " --> pdb=" O   ASN A 355 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   GLN A 357 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N   LEU A 361 " --> pdb=" O   GLN A 357 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 72
      removed outlier: 6.328A  pdb=" N   VAL B  39 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ALA B  38 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
      removed outlier: 8.258A  pdb=" N   ALA B 100 " --> pdb=" O   ALA B  38 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   ILE B  40 " --> pdb=" O   ALA B 100 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   PHE B  99 " --> pdb=" O   ILE B 126 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   GLY B 128 " --> pdb=" O   PHE B  99 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   ASP B 101 " --> pdb=" O   GLY B 128 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 202 through 203
      removed outlier: 6.308A  pdb=" N   SER B 170 " --> pdb=" O   LEU B 229 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   TYR B 231 " --> pdb=" O   SER B 170 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   VAL B 172 " --> pdb=" O   TYR B 231 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ILE B 228 " --> pdb=" O   THR B 255 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   VAL B 280 " --> pdb=" O   VAL B 258 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU B 362 " --> pdb=" O   TRP B 379 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   LEU B 366 " --> pdb=" O   ARG B 375 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   ARG B 375 " --> pdb=" O   LEU B 366 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 343 through 344
      removed outlier: 3.951A  pdb=" N   PHE B 344 " --> pdb=" O   ARG B 347 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 20 through 21
      removed outlier: 3.718A  pdb=" N   LEU H  20 " --> pdb=" O   LEU H  81 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 51 through 52
    Processing sheet with id=AA9, first strand: chain 'H' and resid 39 through 40
    Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AB2, first strand: chain 'L' and resid 46 through 50
      removed outlier: 6.631A  pdb=" N   TRP L  36 " --> pdb=" O   VAL L  48 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER L  93 " --> pdb=" O   VAL L 100 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL L 100 " --> pdb=" O   SER L  93 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 46 through 50
      removed outlier: 6.631A  pdb=" N   TRP L  36 " --> pdb=" O   VAL L  48 " (cutoff:3.500A)

    253 hydrogen bonds defined for protein.
    702 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: 1.73

  Time building geometry restraints manager: 1.90 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: 2263
        1.34 -     1.46: 1659
        1.46 -     1.58: 3053
        1.58 -     1.71: 0
        1.71 -     1.83: 45
  Bond restraints: 7020
  Sorted by residual:
  bond pdb=" CA  ILE L  29 "
       pdb=" CB  ILE L  29 "
    ideal  model  delta    sigma   weight residual
    1.527  1.547 -0.020 1.31e-02 5.83e+03 2.43e+00
  bond pdb=" CA  VAL B 258 "
       pdb=" CB  VAL B 258 "
    ideal  model  delta    sigma   weight residual
    1.547  1.536  0.011 1.10e-02 8.26e+03 1.02e+00
  bond pdb=" CB  GLU L  51 "
       pdb=" CG  GLU L  51 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.36e-01
  bond pdb=" CB  ASP B 138 "
       pdb=" CG  ASP B 138 "
    ideal  model  delta    sigma   weight residual
    1.516  1.537 -0.021 2.50e-02 1.60e+03 6.89e-01
  bond pdb=" CD  GLU L  51 "
       pdb=" OE1 GLU L  51 "
    ideal  model  delta    sigma   weight residual
    1.249  1.234  0.015 1.90e-02 2.77e+03 6.45e-01
  ... (remaining 7015 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 9347
        1.66 -     3.32: 197
        3.32 -     4.98: 31
        4.98 -     6.64: 10
        6.64 -     8.30: 6
  Bond angle restraints: 9591
  Sorted by residual:
  angle pdb=" N   VAL B 376 "
        pdb=" CA  VAL B 376 "
        pdb=" C   VAL B 376 "
      ideal   model   delta    sigma   weight residual
     113.71  110.66    3.05 9.50e-01 1.11e+00 1.03e+01
  angle pdb=" N   GLY H  56 "
        pdb=" CA  GLY H  56 "
        pdb=" C   GLY H  56 "
      ideal   model   delta    sigma   weight residual
     113.18  120.59   -7.41 2.37e+00 1.78e-01 9.78e+00
  angle pdb=" CA  ILE L  29 "
        pdb=" CB  ILE L  29 "
        pdb=" CG1 ILE L  29 "
      ideal   model   delta    sigma   weight residual
     110.40  115.64   -5.24 1.70e+00 3.46e-01 9.51e+00
  angle pdb=" C   GLU A 213 "
        pdb=" N   LEU A 214 "
        pdb=" CA  LEU A 214 "
      ideal   model   delta    sigma   weight residual
     121.54  116.32    5.22 1.91e+00 2.74e-01 7.48e+00
  angle pdb=" C   THR H  23 "
        pdb=" N   VAL H  24 "
        pdb=" CA  VAL H  24 "
      ideal   model   delta    sigma   weight residual
     121.97  126.79   -4.82 1.80e+00 3.09e-01 7.16e+00
  ... (remaining 9586 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 3545
       17.51 -    35.02: 459
       35.02 -    52.53: 126
       52.53 -    70.04: 18
       70.04 -    87.55: 7
  Dihedral angle restraints: 4155
    sinusoidal: 1429
      harmonic: 2726
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -133.41   47.41     1      1.00e+01 1.00e-02 3.10e+01
  dihedral pdb=" CA  GLU A 215 "
           pdb=" C   GLU A 215 "
           pdb=" N   ALA A 216 "
           pdb=" CA  ALA A 216 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.63  -21.37     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CB  CYS L  22 "
           pdb=" SG  CYS L  22 "
           pdb=" SG  CYS L  91 "
           pdb=" CB  CYS L  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   58.31   34.69     1      1.00e+01 1.00e-02 1.71e+01
  ... (remaining 4152 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 825
       0.042 -    0.084: 216
       0.084 -    0.126: 79
       0.126 -    0.169: 7
       0.169 -    0.211: 3
  Chirality restraints: 1130
  Sorted by residual:
  chirality pdb=" CB  ILE B  35 "
            pdb=" CA  ILE B  35 "
            pdb=" CG1 ILE B  35 "
            pdb=" CG2 ILE B  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  GLU L  51 "
            pdb=" N   GLU L  51 "
            pdb=" C   GLU L  51 "
            pdb=" CB  GLU L  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.53e-01
  chirality pdb=" CB  ILE B 190 "
            pdb=" CA  ILE B 190 "
            pdb=" CG1 ILE B 190 "
            pdb=" CG2 ILE B 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.08e-01
  ... (remaining 1127 not shown)

  Planarity restraints: 1230
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 289 "   -0.036 5.00e-02 4.00e+02   5.40e-02 4.67e+00
        pdb=" N   PRO B 290 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B 290 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 290 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 318 "   -0.025 5.00e-02 4.00e+02   3.81e-02 2.32e+00
        pdb=" N   PRO A 319 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 319 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 319 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  50 "   -0.008 2.00e-02 2.50e+03   1.05e-02 2.21e+00
        pdb=" CG  TYR L  50 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  50 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  50 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  50 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  50 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  50 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR L  50 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1227 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 961
        2.76 -     3.29: 6587
        3.29 -     3.83: 10529
        3.83 -     4.36: 10885
        4.36 -     4.90: 19889
  Nonbonded interactions: 48851
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG L  24 "
            pdb=" O   SER L  26 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" OG  SER B 149 "
            pdb=" OE1 GLN B 152 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   MET B  89 "
            pdb=" OG  SER B 319 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" ND2 ASN L  32 "
            pdb=" O   TYR L  94 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" NH2 ARG L  40 "
            pdb=" O   GLU L  84 "
     model   vdw
     2.291 3.120
  ... (remaining 48846 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=0.18 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:             10.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.980
  Find NCS groups from input model:        0.100
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
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      :  0.002   0.029   7020  Z= 0.158
  Angle     :  0.614   8.302   9591  Z= 0.313
  Chirality :  0.044   0.211   1130
  Planarity :  0.004   0.054   1230
  Dihedral  : 17.029  87.552   2389
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.09 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 35.98 %
    Favored  : 63.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.64 (0.27), residues: 934
  helix:  1.11 (0.33), residues: 249
  sheet: -1.06 (0.36), residues: 222
  loop : -2.44 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 381 
 HIS   0.001   0.000   HIS H  54 
 PHE   0.008   0.001   PHE A 197 
 TYR   0.026   0.001   TYR L  50 
 ARG   0.004   0.000   ARG L  24 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 145
  time to evaluate  : 0.702 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 147
  average time/residue: 0.1659
  time to fit residues: 33.6660
Evaluate side-chains
  143 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 139
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain B residue   94 ILE
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain L residue   51 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.4980
   chunk 69 optimal weight:    0.0060
   chunk 38 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0870
   chunk 47 optimal weight:    0.8980
   chunk 37 optimal weight:   10.0000
   chunk 72 optimal weight:    0.3980
   chunk 27 optimal weight:    0.1980
   chunk 43 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 83 optimal weight:   20.0000
   overall best weight:    0.2374

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

Flipped N/Q/H residues before XYZ refinement:
A 101 HIS
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.0770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7020  Z= 0.147
  Angle     :  0.577  13.483   9591  Z= 0.291
  Chirality :  0.043   0.156   1130
  Planarity :  0.004   0.054   1230
  Dihedral  :  4.194  35.515   1009
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.23 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 30.84 %
    Favored  : 63.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.50 (0.27), residues: 934
  helix:  1.05 (0.33), residues: 255
  sheet: -0.76 (0.37), residues: 211
  loop : -2.38 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  34 
 HIS   0.001   0.000   HIS A 293 
 PHE   0.014   0.001   PHE A 152 
 TYR   0.017   0.001   TYR L  50 
 ARG   0.008   0.000   ARG L  24 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 155
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A  132 SER cc_start: 0.8831 (OUTLIER) cc_final: 0.8515 (t)
REVERT: A  322 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8179 (tttt)
REVERT: H   44 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8164 (mptt)
  outliers start: 39
  outliers final: 18
  residues processed: 178
  average time/residue: 0.1675
  time to fit residues: 41.0831
Evaluate side-chains
  162 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  322 LYS
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   32 ASN
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   47 THR
Chi-restraints excluded: chain L residue  100 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 69 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0060
   chunk 90 optimal weight:    8.9990
   chunk 74 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.0953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7020  Z= 0.188
  Angle     :  0.599  14.019   9591  Z= 0.301
  Chirality :  0.044   0.172   1130
  Planarity :  0.004   0.053   1230
  Dihedral  :  3.865  21.527   1002
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.30 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  7.34 %
    Allowed  : 28.34 %
    Favored  : 64.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.49 (0.27), residues: 934
  helix:  1.11 (0.33), residues: 255
  sheet: -0.73 (0.37), residues: 218
  loop : -2.44 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  35 
 HIS   0.002   0.000   HIS H  54 
 PHE   0.010   0.001   PHE B 169 
 TYR   0.015   0.001   TYR L  50 
 ARG   0.004   0.000   ARG L  24 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 141
  time to evaluate  : 0.774 
Fit side-chains
REVERT: B  239 TYR cc_start: 0.7039 (t80) cc_final: 0.6785 (t80)
REVERT: H   44 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8181 (mptt)
  outliers start: 50
  outliers final: 30
  residues processed: 173
  average time/residue: 0.1670
  time to fit residues: 39.3076
Evaluate side-chains
  171 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 141
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   94 ILE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   74 LYS
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   47 THR
Chi-restraints excluded: chain L residue  100 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9980
   chunk 83 optimal weight:    0.0030
   chunk 88 optimal weight:    8.9990
   chunk 79 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0770
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.0152

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
A 358 ASN
B 331 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7020  Z= 0.239
  Angle     :  0.612  14.606   9591  Z= 0.310
  Chirality :  0.044   0.158   1130
  Planarity :  0.004   0.055   1230
  Dihedral  :  4.062  22.174   1002
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.16 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  8.66 %
    Allowed  : 27.17 %
    Favored  : 64.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.63 (0.27), residues: 934
  helix:  1.11 (0.33), residues: 254
  sheet: -1.02 (0.36), residues: 226
  loop : -2.49 (0.26), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP H  48 
 HIS   0.003   0.001   HIS H  54 
 PHE   0.024   0.002   PHE A 152 
 TYR   0.015   0.001   TYR L  50 
 ARG   0.003   0.000   ARG L  24 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 59
    poor density    : 143
  time to evaluate  : 0.718 
Fit side-chains
REVERT: L   24 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7519 (ttm-80)
  outliers start: 59
  outliers final: 42
  residues processed: 185
  average time/residue: 0.1623
  time to fit residues: 40.8354
Evaluate side-chains
  181 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 139
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  371 HIS
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   94 ILE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  213 ASP
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain H residue   54 HIS
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   74 LYS
Chi-restraints excluded: chain H residue   80 SER
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain L residue    1 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   22 CYS
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   32 ASN
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   47 THR
Chi-restraints excluded: chain L residue   93 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.5186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   7020  Z= 0.331
  Angle     :  0.682  15.289   9591  Z= 0.345
  Chirality :  0.045   0.162   1130
  Planarity :  0.004   0.057   1230
  Dihedral  :  4.421  22.885   1002
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 10.42 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  9.54 %
    Allowed  : 28.05 %
    Favored  : 62.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.82 (0.27), residues: 934
  helix:  0.86 (0.33), residues: 255
  sheet: -1.10 (0.36), residues: 223
  loop : -2.57 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  48 
 HIS   0.004   0.001   HIS H  54 
 PHE   0.021   0.002   PHE B 169 
 TYR   0.016   0.001   TYR L  50 
 ARG   0.004   0.001   ARG L  40 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 65
    poor density    : 137
  time to evaluate  : 0.789 
Fit side-chains
REVERT: B  157 MET cc_start: 0.7815 (tpp) cc_final: 0.7528 (tpp)
REVERT: B  353 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7804 (pm20)
REVERT: H   44 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8448 (mtmm)
  outliers start: 65
  outliers final: 47
  residues processed: 182
  average time/residue: 0.1705
  time to fit residues: 43.3846
Evaluate side-chains
  182 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 134
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  371 HIS
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   94 ILE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  213 ASP
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain H residue   44 LYS
Chi-restraints excluded: chain H residue   54 HIS
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   64 LEU
Chi-restraints excluded: chain H residue   74 LYS
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain L residue    1 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   22 CYS
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   32 ASN
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   47 THR
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   93 SER
Chi-restraints excluded: chain L residue  100 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0020
   chunk 21 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.6588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7020  Z= 0.185
  Angle     :  0.621  14.944   9591  Z= 0.309
  Chirality :  0.044   0.180   1130
  Planarity :  0.004   0.055   1230
  Dihedral  :  4.170  21.971   1002
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.95 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  7.34 %
    Allowed  : 30.69 %
    Favored  : 61.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.69 (0.27), residues: 934
  helix:  0.92 (0.32), residues: 255
  sheet: -0.92 (0.37), residues: 217
  loop : -2.51 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  48 
 HIS   0.002   0.000   HIS H  54 
 PHE   0.015   0.001   PHE B 241 
 TYR   0.015   0.001   TYR L  50 
 ARG   0.004   0.000   ARG L  24 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 139
  time to evaluate  : 0.821 
Fit side-chains
REVERT: A  275 LYS cc_start: 0.8199 (mmpt) cc_final: 0.7952 (mptt)
REVERT: A  320 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8834 (tt)
REVERT: A  392 TYR cc_start: 0.6397 (OUTLIER) cc_final: 0.5832 (t80)
REVERT: B  239 TYR cc_start: 0.7210 (t80) cc_final: 0.6993 (t80)
REVERT: L   24 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.8001 (ttm-80)
  outliers start: 50
  outliers final: 40
  residues processed: 174
  average time/residue: 0.1596
  time to fit residues: 38.2824
Evaluate side-chains
  177 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 135
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  371 HIS
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   94 ILE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  213 ASP
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain H residue   54 HIS
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   74 LYS
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain L residue    1 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   22 CYS
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   32 ASN
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   47 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 74 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 88 optimal weight:   10.0000
   chunk 55 optimal weight:    0.3980
   chunk 54 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7020  Z= 0.199
  Angle     :  0.637  13.936   9591  Z= 0.315
  Chirality :  0.044   0.183   1130
  Planarity :  0.004   0.056   1230
  Dihedral  :  4.104  21.787   1002
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.49 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  7.78 %
    Allowed  : 30.54 %
    Favored  : 61.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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 (0.27), residues: 934
  helix:  0.96 (0.32), residues: 255
  sheet: -0.96 (0.37), residues: 220
  loop : -2.50 (0.26), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  35 
 HIS   0.002   0.000   HIS H  54 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.015   0.001   TYR L  50 
 ARG   0.004   0.000   ARG L  24 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 137
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A  275 LYS cc_start: 0.8184 (mmpt) cc_final: 0.7938 (mptt)
REVERT: H   44 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8427 (mtmm)
REVERT: L   24 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.6800 (ttt90)
  outliers start: 53
  outliers final: 43
  residues processed: 175
  average time/residue: 0.1691
  time to fit residues: 40.9838
Evaluate side-chains
  181 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 137
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  371 HIS
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   94 ILE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  213 ASP
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain H residue   44 LYS
Chi-restraints excluded: chain H residue   54 HIS
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   74 LYS
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain L residue    1 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   22 CYS
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   32 ASN
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   47 THR
Chi-restraints excluded: chain L residue  100 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 26 optimal weight:    0.0170
   chunk 17 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0050
   chunk 69 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   chunk 84 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.4232

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7020  Z= 0.170
  Angle     :  0.638  13.595   9591  Z= 0.314
  Chirality :  0.044   0.191   1130
  Planarity :  0.004   0.055   1230
  Dihedral  :  3.988  20.885   1002
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.77 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  7.49 %
    Allowed  : 30.10 %
    Favored  : 62.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.59 (0.27), residues: 934
  helix:  0.96 (0.32), residues: 257
  sheet: -0.85 (0.37), residues: 220
  loop : -2.43 (0.26), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 285 
 HIS   0.001   0.000   HIS H  54 
 PHE   0.021   0.001   PHE B 241 
 TYR   0.019   0.001   TYR B 239 
 ARG   0.004   0.000   ARG L  24 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 140
  time to evaluate  : 0.787 
Fit side-chains
REVERT: A  132 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8695 (t)
REVERT: A  275 LYS cc_start: 0.8116 (mmpt) cc_final: 0.7901 (mptt)
REVERT: A  320 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8806 (tt)
REVERT: A  392 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.5709 (t80)
REVERT: B  158 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7585 (mt)
REVERT: B  371 ARG cc_start: 0.8034 (mmm-85) cc_final: 0.7546 (mmt90)
REVERT: H   44 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8127 (mptt)
REVERT: L   24 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.7913 (ttm-80)
  outliers start: 51
  outliers final: 40
  residues processed: 174
  average time/residue: 0.1570
  time to fit residues: 37.5628
Evaluate side-chains
  182 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 137
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  371 HIS
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   94 ILE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  165 ASP
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  213 ASP
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain H residue   44 LYS
Chi-restraints excluded: chain H residue   54 HIS
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   74 LYS
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain L residue    1 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   22 CYS
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   32 ASN
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   47 THR
Chi-restraints excluded: chain L residue   93 SER
Chi-restraints excluded: chain L residue  100 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0020
   chunk 25 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    0.6992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7020  Z= 0.201
  Angle     :  0.640  13.198   9591  Z= 0.317
  Chirality :  0.044   0.186   1130
  Planarity :  0.004   0.055   1230
  Dihedral  :  4.027  21.183   1002
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.59 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  7.05 %
    Allowed  : 30.98 %
    Favored  : 61.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.60 (0.27), residues: 934
  helix:  1.02 (0.32), residues: 255
  sheet: -0.85 (0.38), residues: 220
  loop : -2.47 (0.26), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 285 
 HIS   0.002   0.000   HIS H  54 
 PHE   0.013   0.001   PHE B 241 
 TYR   0.016   0.001   TYR L  50 
 ARG   0.006   0.000   ARG B  67 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 142
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A  132 SER cc_start: 0.8965 (OUTLIER) cc_final: 0.8699 (t)
REVERT: A  275 LYS cc_start: 0.8164 (mmpt) cc_final: 0.7927 (mptt)
REVERT: A  320 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8818 (tt)
REVERT: B  158 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7641 (mt)
REVERT: B  371 ARG cc_start: 0.8062 (mmm-85) cc_final: 0.7721 (mmt90)
REVERT: H   44 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8088 (mptt)
REVERT: L   24 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7975 (ttm-80)
  outliers start: 48
  outliers final: 41
  residues processed: 175
  average time/residue: 0.1542
  time to fit residues: 37.4361
Evaluate side-chains
  184 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 139
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  371 HIS
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   94 ILE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  165 ASP
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  213 ASP
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain H residue   44 LYS
Chi-restraints excluded: chain H residue   54 HIS
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   74 LYS
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain L residue    1 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   22 CYS
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   32 ASN
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   47 THR
Chi-restraints excluded: chain L residue   93 SER
Chi-restraints excluded: chain L residue  100 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0980
   chunk 7 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 77 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7020  Z= 0.196
  Angle     :  0.652  13.054   9591  Z= 0.323
  Chirality :  0.044   0.186   1130
  Planarity :  0.004   0.055   1230
  Dihedral  :  4.004  21.177   1002
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.95 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  7.49 %
    Allowed  : 30.54 %
    Favored  : 61.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.59 (0.27), residues: 934
  helix:  1.00 (0.32), residues: 256
  sheet: -0.82 (0.38), residues: 222
  loop : -2.49 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP H  48 
 HIS   0.002   0.000   HIS H  54 
 PHE   0.021   0.001   PHE B 241 
 TYR   0.016   0.001   TYR B 239 
 ARG   0.005   0.000   ARG B  67 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 135
  time to evaluate  : 0.782 
Fit side-chains
REVERT: A  132 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8728 (t)
REVERT: A  275 LYS cc_start: 0.8135 (mmpt) cc_final: 0.7906 (mptt)
REVERT: A  320 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8814 (tt)
REVERT: A  392 TYR cc_start: 0.6280 (OUTLIER) cc_final: 0.5694 (t80)
REVERT: B  157 MET cc_start: 0.7591 (tpp) cc_final: 0.6914 (tpp)
REVERT: B  158 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7613 (mt)
REVERT: B  371 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7677 (mmt90)
REVERT: H   44 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8082 (mptt)
REVERT: L   24 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7932 (ttm-80)
  outliers start: 51
  outliers final: 41
  residues processed: 169
  average time/residue: 0.1704
  time to fit residues: 40.4167
Evaluate side-chains
  180 residues out of total 822 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 134
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  371 HIS
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   94 ILE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  165 ASP
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  213 ASP
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain H residue   44 LYS
Chi-restraints excluded: chain H residue   54 HIS
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   74 LYS
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain L residue    1 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   32 ASN
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   47 THR
Chi-restraints excluded: chain L residue   93 SER
Chi-restraints excluded: chain L residue  100 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0770
   chunk 73 optimal weight:    0.0070
   chunk 30 optimal weight:    0.8980
   chunk 75 optimal weight:    0.0270
   chunk 9 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0000
   chunk 64 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.2018

-------------------------------------------------------------------------------
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 = 0.4072 r_free = 0.4072 target = 0.173448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.145099 restraints weight = 26788.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.145677 restraints weight = 22039.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.144325 restraints weight = 9942.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3761
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3761 r_free = 0.3761    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3761 r_free = 0.3761    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3761
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7020  Z= 0.159
  Angle     :  0.630  13.001   9591  Z= 0.310
  Chirality :  0.044   0.196   1130
  Planarity :  0.004   0.055   1230
  Dihedral  :  3.814  19.812   1002
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.98 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 32.31 %
    Favored  : 62.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.43 (0.27), residues: 934
  helix:  1.04 (0.33), residues: 258
  sheet: -0.68 (0.38), residues: 220
  loop : -2.36 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP H  48 
 HIS   0.002   0.000   HIS A  67 
 PHE   0.024   0.001   PHE B 241 
 TYR   0.020   0.001   TYR B 239 
 ARG   0.004   0.000   ARG B  67 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1812.39 seconds
wall clock time: 33 minutes 19.18 seconds (1999.18 seconds total)