Starting phenix.real_space_refine
on Wed Feb 12 04:20:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wvw_32860/02_2025/7wvw_32860.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wvw_32860/02_2025/7wvw_32860.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wvw_32860/02_2025/7wvw_32860.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wvw_32860/02_2025/7wvw_32860.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wvw_32860/02_2025/7wvw_32860.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wvw_32860/02_2025/7wvw_32860.cif"
  }
  resolution = 3.1
  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=   0.004
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      54      5.16       5
     C    4608      2.51       5
     N    1212      2.21       5
     O    1295      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7169
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 65
          Classifications: {'peptide': 7}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 2344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2344
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 13, 'TRANS': 285}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "A"
      Number of atoms: 1753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1753
          Classifications: {'peptide': 223}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 2, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "B"
      Number of atoms: 2583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2583
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 424
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 4.13, per 1000 atoms: 0.58
  Number of scatterers: 7169
  At special positions: 0
  Unit cell: (114.95, 119.13, 84.645, 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      54     16.00
     O    1295      8.00
     N    1212      7.00
     C    4608      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 176 " 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: 1.55
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1734

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      48.3% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'R' and resid 20 through 55
      Proline residue:  R  29  - end of helix
      removed outlier: 3.737A  pdb=" N   PHE R  53 " --> pdb=" O   TRP R  49 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 58 through 87
      Proline residue:  R  79  - end of helix
    Processing helix  chain 'R' and resid 94 through 129
    Processing helix  chain 'R' and resid 129 through 136
    Processing helix  chain 'R' and resid 138 through 163
      removed outlier: 4.089A  pdb=" N   GLY R 148 " --> pdb=" O   LYS R 144 " (cutoff:3.500A)
      Proline residue:  R 149  - end of helix
      Proline residue:  R 159  - end of helix
    Processing helix  chain 'R' and resid 186 through 209
    Processing helix  chain 'R' and resid 210 through 231
    Processing helix  chain 'R' and resid 237 through 267
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 267 through 274
    Processing helix  chain 'R' and resid 278 through 303
      removed outlier: 4.388A  pdb=" N   ASN R 285 " --> pdb=" O   ASP R 281 " (cutoff:3.500A)
      Proline residue:  R 286  - end of helix
      Proline residue:  R 299  - end of helix
    Processing helix  chain 'R' and resid 306 through 317
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.798A  pdb=" N   GLU A  25 " --> pdb=" O   LYS A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.888A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
      removed outlier: 3.700A  pdb=" N   LYS A 211 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ILE A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 232
      removed outlier: 4.290A  pdb=" N   ASP A 232 " --> pdb=" O   SER A 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 229 through 232'
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 257 through 261
      removed outlier: 4.086A  pdb=" N   THR A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 4.051A  pdb=" N   GLU A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   THR A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   HIS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 287
      removed outlier: 3.819A  pdb=" N   ILE A 286 " --> pdb=" O   PRO A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 312
      removed outlier: 3.687A  pdb=" N   ASN A 312 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 31 through 35
      removed outlier: 3.614A  pdb=" N   ASN B  35 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 23
      removed outlier: 3.653A  pdb=" N   LEU C  15 " --> pdb=" O   GLN C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.783A  pdb=" N   LEU C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   MET C  38 " --> pdb=" O   ALA C  34 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 164 through 168
      removed outlier: 3.501A  pdb=" N   THR R 177 " --> pdb=" O   THR R 165 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187
    Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 187
      removed outlier: 6.075A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 198 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   PHE A 200 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.831A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.548A  pdb=" N   ALA A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.526A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.661A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.625A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.592A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.687A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.734A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.559A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    392 hydrogen bonds defined for protein.
    1131 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: 2.49

  Time building geometry restraints manager: 1.84 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2294
        1.35 -     1.47: 1778
        1.47 -     1.59: 3168
        1.59 -     1.71: 0
        1.71 -     1.83: 79
  Bond restraints: 7319
  Sorted by residual:
  bond pdb=" SD  FME L   1 "
       pdb=" CE  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.805  1.752  0.053 2.00e-02 2.50e+03 6.95e+00
  bond pdb=" CG  FME L   1 "
       pdb=" SD  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.817  1.770  0.047 2.00e-02 2.50e+03 5.50e+00
  bond pdb=" N   FME L   1 "
       pdb=" CN  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.335  1.376 -0.041 2.00e-02 2.50e+03 4.24e+00
  bond pdb=" N   FME L   1 "
       pdb=" CA  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.437  0.021 1.90e-02 2.77e+03 1.26e+00
  bond pdb=" CN  FME L   1 "
       pdb=" O1  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.221  1.241 -0.020 2.00e-02 2.50e+03 9.75e-01
  ... (remaining 7314 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 9792
        1.65 -     3.31: 103
        3.31 -     4.96: 25
        4.96 -     6.62: 7
        6.62 -     8.27: 1
  Bond angle restraints: 9928
  Sorted by residual:
  angle pdb=" C   TYR R 175 "
        pdb=" N   CYS R 176 "
        pdb=" CA  CYS R 176 "
      ideal   model   delta    sigma   weight residual
     122.84  118.55    4.29 1.30e+00 5.92e-01 1.09e+01
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.71  111.03    2.68 9.50e-01 1.11e+00 7.95e+00
  angle pdb=" CA  CYS R 176 "
        pdb=" CB  CYS R 176 "
        pdb=" SG  CYS R 176 "
      ideal   model   delta    sigma   weight residual
     114.40  120.09   -5.69 2.30e+00 1.89e-01 6.12e+00
  angle pdb=" CA  LEU R 162 "
        pdb=" CB  LEU R 162 "
        pdb=" CG  LEU R 162 "
      ideal   model   delta    sigma   weight residual
     116.30  124.57   -8.27 3.50e+00 8.16e-02 5.58e+00
  angle pdb=" C   ASP A 329 "
        pdb=" N   THR A 330 "
        pdb=" CA  THR A 330 "
      ideal   model   delta    sigma   weight residual
     122.08  125.17   -3.09 1.47e+00 4.63e-01 4.41e+00
  ... (remaining 9923 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.27: 3850
       16.27 -    32.54: 361
       32.54 -    48.81: 88
       48.81 -    65.08: 9
       65.08 -    81.35: 7
  Dihedral angle restraints: 4315
    sinusoidal: 1641
      harmonic: 2674
  Sorted by residual:
  dihedral pdb=" CA  PHE R 161 "
           pdb=" C   PHE R 161 "
           pdb=" N   LEU R 162 "
           pdb=" CA  LEU R 162 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.92  -17.08     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  ASN A 348 "
           pdb=" CB  ASN A 348 "
           pdb=" CG  ASN A 348 "
           pdb=" OD1 ASN A 348 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -177.28  -62.72     2      2.00e+01 2.50e-03 9.48e+00
  dihedral pdb=" CB  MET R 214 "
           pdb=" CG  MET R 214 "
           pdb=" SD  MET R 214 "
           pdb=" CE  MET R 214 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.29  -57.71     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 4312 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 686
       0.027 -    0.053: 280
       0.053 -    0.080: 110
       0.080 -    0.107: 55
       0.107 -    0.133: 28
  Chirality restraints: 1159
  Sorted by residual:
  chirality pdb=" CA  LEU R 162 "
            pdb=" N   LEU R 162 "
            pdb=" C   LEU R 162 "
            pdb=" CB  LEU R 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.45e-01
  chirality pdb=" CA  VAL C  54 "
            pdb=" N   VAL C  54 "
            pdb=" C   VAL C  54 "
            pdb=" CB  VAL C  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.26e-01
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.97e-01
  ... (remaining 1156 not shown)

  Planarity restraints: 1243
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 148 "    0.034 5.00e-02 4.00e+02   5.08e-02 4.14e+00
        pdb=" N   PRO R 149 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO R 149 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R 149 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.023 5.00e-02 4.00e+02   3.53e-02 2.00e+00
        pdb=" N   PRO B 236 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R  95 "   -0.012 2.00e-02 2.50e+03   8.74e-03 1.91e+00
        pdb=" CG  TRP R  95 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP R  95 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TRP R  95 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP R  95 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP R  95 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP R  95 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R  95 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R  95 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP R  95 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1240 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 448
        2.74 -     3.28: 7244
        3.28 -     3.82: 12448
        3.82 -     4.36: 14507
        4.36 -     4.90: 25386
  Nonbonded interactions: 60033
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASN B 110 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OD1 ASN A 270 "
            pdb=" OG1 THR A 325 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OH  TYR A 231 "
            pdb=" OG  SER A 282 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" NH2 ARG B 256 "
            pdb=" OD2 ASP C  36 "
     model   vdw
     2.309 3.120
  ... (remaining 60028 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.750
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.060
  Find NCS groups from input model:        0.090
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
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   0.053   7319  Z= 0.137
  Angle     :  0.496   8.271   9928  Z= 0.266
  Chirality :  0.040   0.133   1159
  Planarity :  0.003   0.051   1243
  Dihedral  : 13.512  81.345   2578
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  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:  0.78 (0.28), residues: 911
  helix:  1.80 (0.26), residues: 413
  sheet:  0.56 (0.45), residues: 152
  loop : -1.09 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP R  95 
 HIS   0.004   0.000   HIS R 102 
 PHE   0.016   0.001   PHE R 161 
 TYR   0.009   0.001   TYR R 175 
 ARG   0.013   0.001   ARG B  96 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.772 
Fit side-chains
REVERT: R  106 ASP cc_start: 0.7299 (t70) cc_final: 0.7097 (t70)
REVERT: R  204 ILE cc_start: 0.7547 (mt) cc_final: 0.6928 (mt)
REVERT: A  325 THR cc_start: 0.7395 (m) cc_final: 0.7172 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.1926
  time to fit residues: 43.6803
Evaluate side-chains
  125 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0270
   chunk 42 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    1.1842

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

Flipped N/Q/H residues before XYZ refinement:
** R 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
B 220 GLN
B 311 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.153251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.119735 restraints weight = 8727.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 2.08
r_work: 0.3296 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7319  Z= 0.272
  Angle     :  0.575   8.192   9928  Z= 0.300
  Chirality :  0.044   0.151   1159
  Planarity :  0.004   0.048   1243
  Dihedral  :  4.111  53.587    984
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 11.72 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.28), residues: 911
  helix:  1.76 (0.25), residues: 424
  sheet:  0.67 (0.41), residues: 170
  loop : -1.10 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 211 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.016   0.002   PHE B 199 
 TYR   0.013   0.002   TYR R 175 
 ARG   0.006   0.000   ARG R  54 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 167
  time to evaluate  : 0.827 
Fit side-chains
REVERT: R  103 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8305 (mp)
REVERT: R  278 LYS cc_start: 0.7860 (mtmt) cc_final: 0.7426 (mttm)
REVERT: B   96 ARG cc_start: 0.8006 (ttm170) cc_final: 0.7630 (mtp-110)
REVERT: B  325 MET cc_start: 0.8323 (tpp) cc_final: 0.8086 (tpp)
  outliers start: 9
  outliers final: 7
  residues processed: 172
  average time/residue: 0.2074
  time to fit residues: 46.9890
Evaluate side-chains
  147 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  103 ILE
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  301 LEU
Chi-restraints excluded: chain B residue  173 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 86 optimal weight:    8.9990
   chunk 84 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 83 optimal weight:    0.7980
   chunk 30 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
R 102 HIS
R 294 ASN
A 245 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.150328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.114492 restraints weight = 8796.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 2.11
r_work: 0.3249 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7319  Z= 0.211
  Angle     :  0.525   7.539   9928  Z= 0.273
  Chirality :  0.042   0.150   1159
  Planarity :  0.004   0.049   1243
  Dihedral  :  4.089  54.210    984
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.84 %
    Favored  : 83.72 %
  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:  1.03 (0.28), residues: 911
  helix:  1.91 (0.25), residues: 425
  sheet:  0.43 (0.40), residues: 183
  loop : -0.92 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 102 
 PHE   0.016   0.001   PHE B 199 
 TYR   0.010   0.001   TYR R 175 
 ARG   0.005   0.000   ARG R  54 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 0.777 
Fit side-chains
REVERT: R  103 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8387 (mp)
REVERT: R  278 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7465 (mttm)
REVERT: A  242 ASN cc_start: 0.7374 (t0) cc_final: 0.6772 (t0)
REVERT: A  270 ASN cc_start: 0.8523 (m-40) cc_final: 0.8266 (m-40)
  outliers start: 11
  outliers final: 8
  residues processed: 150
  average time/residue: 0.1771
  time to fit residues: 36.2017
Evaluate side-chains
  145 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  103 ILE
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 89 optimal weight:    0.3980
   chunk 38 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 85 optimal weight:    9.9990
   chunk 60 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.6982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.149555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.114291 restraints weight = 8834.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.07
r_work: 0.3233 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7319  Z= 0.191
  Angle     :  0.513   9.840   9928  Z= 0.263
  Chirality :  0.041   0.134   1159
  Planarity :  0.004   0.049   1243
  Dihedral  :  4.077  55.026    984
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.49 %
    Favored  : 82.42 %
  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:  1.02 (0.29), residues: 911
  helix:  1.91 (0.25), residues: 426
  sheet:  0.32 (0.39), residues: 192
  loop : -0.90 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.011   0.001   TYR R 175 
 ARG   0.003   0.000   ARG R  54 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 0.852 
Fit side-chains
REVERT: R   27 ILE cc_start: 0.7227 (mm) cc_final: 0.6892 (mt)
REVERT: R  143 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.6565 (mpt)
REVERT: R  273 PHE cc_start: 0.8109 (m-10) cc_final: 0.7834 (m-80)
REVERT: R  278 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7481 (mttm)
REVERT: A   25 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6950 (mp0)
REVERT: B  228 ASP cc_start: 0.8632 (m-30) cc_final: 0.8402 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 159
  average time/residue: 0.2579
  time to fit residues: 53.2230
Evaluate side-chains
  149 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 137
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  303 VAL
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 77 optimal weight:    0.7980
   chunk 80 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3847 r_free = 0.3847 target = 0.152076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.117674 restraints weight = 8603.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.00
r_work: 0.3280 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7319  Z= 0.209
  Angle     :  0.517   8.678   9928  Z= 0.266
  Chirality :  0.041   0.133   1159
  Planarity :  0.004   0.049   1243
  Dihedral  :  4.125  55.105    984
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 16.67 %
    Favored  : 81.25 %
  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:  0.89 (0.28), residues: 911
  helix:  1.85 (0.25), residues: 426
  sheet:  0.11 (0.38), residues: 193
  loop : -0.93 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.013   0.001   TYR R 221 
 ARG   0.008   0.000   ARG R 238 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.871 
Fit side-chains
REVERT: R   27 ILE cc_start: 0.7307 (mm) cc_final: 0.6926 (mt)
REVERT: R   99 LYS cc_start: 0.8241 (tptm) cc_final: 0.7941 (mmtt)
REVERT: R  143 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7085 (mpp)
REVERT: R  192 LYS cc_start: 0.7886 (tptp) cc_final: 0.7425 (mttp)
REVERT: R  273 PHE cc_start: 0.8091 (m-10) cc_final: 0.7820 (m-80)
REVERT: A   25 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7147 (mp0)
REVERT: B   44 GLN cc_start: 0.7409 (tm-30) cc_final: 0.7179 (tm-30)
REVERT: B  188 MET cc_start: 0.7893 (mmm) cc_final: 0.7585 (mmm)
REVERT: C   31 SER cc_start: 0.8393 (m) cc_final: 0.8078 (p)
  outliers start: 16
  outliers final: 10
  residues processed: 149
  average time/residue: 0.1865
  time to fit residues: 37.6449
Evaluate side-chains
  146 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 86 optimal weight:    0.2980
   chunk 42 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B 311 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.145542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.109983 restraints weight = 8774.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.03
r_work: 0.3173 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7319  Z= 0.243
  Angle     :  0.531   9.011   9928  Z= 0.273
  Chirality :  0.042   0.161   1159
  Planarity :  0.004   0.048   1243
  Dihedral  :  4.209  55.397    984
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.84 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.28), residues: 911
  helix:  1.80 (0.25), residues: 427
  sheet:  0.01 (0.38), residues: 191
  loop : -0.98 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.012   0.001   TYR R 221 
 ARG   0.006   0.000   ARG R 238 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.797 
Fit side-chains
REVERT: R   27 ILE cc_start: 0.7274 (mm) cc_final: 0.6892 (mt)
REVERT: R   99 LYS cc_start: 0.8257 (tptm) cc_final: 0.8011 (mmtt)
REVERT: R  143 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.6924 (mpp)
REVERT: R  161 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7727 (m-80)
REVERT: R  273 PHE cc_start: 0.8171 (m-10) cc_final: 0.7859 (m-80)
REVERT: A   25 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7146 (mp0)
REVERT: B  188 MET cc_start: 0.7971 (mmm) cc_final: 0.7729 (mmm)
REVERT: C   31 SER cc_start: 0.8426 (m) cc_final: 0.8121 (p)
  outliers start: 21
  outliers final: 15
  residues processed: 152
  average time/residue: 0.1868
  time to fit residues: 38.2448
Evaluate side-chains
  151 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  161 PHE
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  303 VAL
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 65 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0020
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
B 311 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.146420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.111440 restraints weight = 8589.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.01
r_work: 0.3191 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7319  Z= 0.196
  Angle     :  0.517   9.399   9928  Z= 0.266
  Chirality :  0.041   0.130   1159
  Planarity :  0.004   0.049   1243
  Dihedral  :  4.187  55.552    984
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.97 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.28), residues: 911
  helix:  1.82 (0.25), residues: 427
  sheet: -0.02 (0.38), residues: 189
  loop : -0.95 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.002   0.001   HIS B 225 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.004   0.000   ARG R 238 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.834 
Fit side-chains
REVERT: R   27 ILE cc_start: 0.7117 (mm) cc_final: 0.6710 (mt)
REVERT: R   99 LYS cc_start: 0.8286 (tptm) cc_final: 0.8065 (mmtt)
REVERT: R  143 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.6929 (mpp)
REVERT: R  161 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7787 (m-80)
REVERT: R  273 PHE cc_start: 0.8152 (m-10) cc_final: 0.7829 (m-80)
REVERT: A   25 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6706 (mp0)
REVERT: B  188 MET cc_start: 0.7930 (mmm) cc_final: 0.7570 (mmm)
REVERT: C   31 SER cc_start: 0.8416 (m) cc_final: 0.8135 (p)
  outliers start: 23
  outliers final: 15
  residues processed: 146
  average time/residue: 0.1835
  time to fit residues: 36.3691
Evaluate side-chains
  147 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  161 PHE
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  303 VAL
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 53 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0270
   chunk 13 optimal weight:    0.3980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
B 311 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.147152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.112396 restraints weight = 8733.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 2.01
r_work: 0.3204 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7319  Z= 0.176
  Angle     :  0.526   9.485   9928  Z= 0.268
  Chirality :  0.041   0.141   1159
  Planarity :  0.004   0.048   1243
  Dihedral  :  4.161  55.529    984
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.62 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.28), residues: 911
  helix:  1.84 (0.25), residues: 427
  sheet: -0.05 (0.40), residues: 170
  loop : -0.90 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.002   0.001   HIS B 225 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.009   0.001   TYR R 221 
 ARG   0.004   0.000   ARG R 238 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 1.029 
Fit side-chains
REVERT: R   99 LYS cc_start: 0.8282 (tptm) cc_final: 0.8081 (mmtt)
REVERT: R  143 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.6874 (mpp)
REVERT: R  161 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7707 (m-80)
REVERT: R  273 PHE cc_start: 0.8151 (m-10) cc_final: 0.7824 (m-80)
REVERT: A   25 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6680 (mp0)
REVERT: B  188 MET cc_start: 0.7847 (mmm) cc_final: 0.7577 (mmm)
REVERT: C   31 SER cc_start: 0.8409 (m) cc_final: 0.8123 (p)
  outliers start: 20
  outliers final: 15
  residues processed: 142
  average time/residue: 0.1936
  time to fit residues: 37.3877
Evaluate side-chains
  149 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  161 PHE
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  303 VAL
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 85 optimal weight:   10.0000
   chunk 32 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 311 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.145412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.110561 restraints weight = 8755.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.01
r_work: 0.3177 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3031 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7319  Z= 0.219
  Angle     :  0.539   9.573   9928  Z= 0.276
  Chirality :  0.042   0.137   1159
  Planarity :  0.004   0.048   1243
  Dihedral  :  4.205  55.995    984
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.62 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.29), residues: 911
  helix:  1.86 (0.25), residues: 427
  sheet: -0.10 (0.38), residues: 189
  loop : -0.92 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.018   0.001   TYR B  59 
 ARG   0.004   0.000   ARG R 238 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 1.133 
Fit side-chains
REVERT: R   99 LYS cc_start: 0.8313 (tptm) cc_final: 0.8104 (mmtt)
REVERT: R  143 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.6919 (mpp)
REVERT: R  161 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7750 (m-80)
REVERT: R  273 PHE cc_start: 0.8141 (m-10) cc_final: 0.7813 (m-80)
REVERT: A   25 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6593 (mp0)
REVERT: B  188 MET cc_start: 0.7918 (mmm) cc_final: 0.7643 (mmm)
REVERT: C   31 SER cc_start: 0.8429 (m) cc_final: 0.8151 (p)
  outliers start: 22
  outliers final: 18
  residues processed: 143
  average time/residue: 0.2033
  time to fit residues: 39.8402
Evaluate side-chains
  149 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue   54 ARG
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  161 PHE
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  303 VAL
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 14 optimal weight:    0.0970
   chunk 10 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 89 optimal weight:    0.4980
   chunk 87 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
B 311 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.146435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.111717 restraints weight = 8908.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 1.99
r_work: 0.3194 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.3644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7319  Z= 0.190
  Angle     :  0.538   9.886   9928  Z= 0.274
  Chirality :  0.041   0.130   1159
  Planarity :  0.004   0.049   1243
  Dihedral  :  4.190  56.145    984
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.49 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.28), residues: 911
  helix:  1.86 (0.25), residues: 427
  sheet: -0.16 (0.39), residues: 179
  loop : -0.86 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.016   0.001   TYR A 231 
 ARG   0.004   0.000   ARG R 238 

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.635 
Fit side-chains
REVERT: R   33 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6939 (mp)
REVERT: R   99 LYS cc_start: 0.8338 (tptm) cc_final: 0.8138 (mmtt)
REVERT: R  143 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.6935 (mpp)
REVERT: R  161 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7767 (m-80)
REVERT: R  273 PHE cc_start: 0.8081 (m-10) cc_final: 0.7767 (m-80)
REVERT: A   25 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6694 (mp0)
REVERT: B   13 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8200 (pt0)
REVERT: B  188 MET cc_start: 0.7876 (mmm) cc_final: 0.7606 (mmm)
REVERT: C   31 SER cc_start: 0.8455 (m) cc_final: 0.8190 (p)
  outliers start: 22
  outliers final: 16
  residues processed: 146
  average time/residue: 0.1874
  time to fit residues: 36.9533
Evaluate side-chains
  151 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  161 PHE
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  303 VAL
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0070
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.9000

-------------------------------------------------------------------------------
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 = 0.3756 r_free = 0.3756 target = 0.145078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.109403 restraints weight = 8727.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.05
r_work: 0.3162 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7319  Z= 0.229
  Angle     :  0.557   9.798   9928  Z= 0.286
  Chirality :  0.042   0.139   1159
  Planarity :  0.004   0.048   1243
  Dihedral  :  4.259  56.740    984
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 18.75 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.29), residues: 911
  helix:  1.81 (0.25), residues: 429
  sheet: -0.14 (0.38), residues: 189
  loop : -0.89 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.016   0.001   TYR A 231 
 ARG   0.004   0.000   ARG R 238 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4550.37 seconds
wall clock time: 81 minutes 44.66 seconds (4904.66 seconds total)