Starting phenix.real_space_refine
on Wed Feb 12 23:27:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y15_33557/02_2025/7y15_33557.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y15_33557/02_2025/7y15_33557.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y15_33557/02_2025/7y15_33557.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y15_33557/02_2025/7y15_33557.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y15_33557/02_2025/7y15_33557.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y15_33557/02_2025/7y15_33557.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.087
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      69      5.16       5
     C    5428      2.51       5
     N    1453      2.21       5
     O    1545      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8495
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1654
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 1, 'TRANS': 216}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 85
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 66
    Chain: "B"
      Number of atoms: 2553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2553
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 435
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 2053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2053
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 10, 'TRANS': 253}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 40
    Chain: "S"
      Number of atoms: 1746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1746
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 54
          Unusual residues: {'PLM': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.67, per 1000 atoms: 0.67
  Number of scatterers: 8495
  At special positions: 0
  Unit cell: (122.85, 84.375, 125.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      69     16.00
     O    1545      8.00
     N    1453      7.00
     C    5428      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 164 " - pdb=" SG  CYS R 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.17
  Conformation dependent library (CDL) restraints added in 972.5 milliseconds
  

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2082

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 13 sheets defined
      37.1% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 30
      removed outlier: 3.599A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA A  30 " --> pdb=" O   ASP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 51
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.214A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.564A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 308
    Processing helix  chain 'A' and resid 329 through 352
      removed outlier: 4.588A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.589A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.538A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 282
      No H-bonds generated for 'chain 'B' and resid 280 through 282'
    Processing helix  chain 'C' and resid 8 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
      removed outlier: 3.504A  pdb=" N   ASN C  59 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 23 through 53
    Processing helix  chain 'R' and resid 61 through 87
      removed outlier: 3.781A  pdb=" N   ILE R  65 " --> pdb=" O   PHE R  61 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   THR R  87 " --> pdb=" O   LEU R  83 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 96 through 129
      removed outlier: 3.678A  pdb=" N   VAL R 127 " --> pdb=" O   ARG R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 136
    Processing helix  chain 'R' and resid 140 through 165
      removed outlier: 4.497A  pdb=" N   PHE R 163 " --> pdb=" O   LEU R 159 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 209
      Proline residue:  R 192  - end of helix
    Processing helix  chain 'R' and resid 216 through 234
    Processing helix  chain 'R' and resid 234 through 245
      removed outlier: 4.234A  pdb=" N   SER R 238 " --> pdb=" O   SER R 234 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   TYR R 245 " --> pdb=" O   TRP R 241 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 253 through 277
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 4.182A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.237A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.342A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.279A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.556A  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: 3.703A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.056A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.964A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.650A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.036A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.573A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.587A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.610A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.913A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.546A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.973A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.973A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129
      removed outlier: 3.664A  pdb=" N   ALA S 199 " --> pdb=" O   SER S 196 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 135 through 136
      removed outlier: 6.605A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    440 hydrogen bonds defined for protein.
    1242 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: 2.57

  Time building geometry restraints manager: 2.54 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2712
        1.34 -     1.46: 2133
        1.46 -     1.58: 3726
        1.58 -     1.70: 0
        1.70 -     1.82: 100
  Bond restraints: 8671
  Sorted by residual:
  bond pdb=" C1  PLM R 403 "
       pdb=" C2  PLM R 403 "
    ideal  model  delta    sigma   weight residual
    1.542  1.508  0.034 2.00e-02 2.50e+03 2.82e+00
  bond pdb=" C1  PLM R 401 "
       pdb=" C2  PLM R 401 "
    ideal  model  delta    sigma   weight residual
    1.542  1.509  0.033 2.00e-02 2.50e+03 2.69e+00
  bond pdb=" C1  PLM R 402 "
       pdb=" C2  PLM R 402 "
    ideal  model  delta    sigma   weight residual
    1.542  1.510  0.032 2.00e-02 2.50e+03 2.62e+00
  bond pdb=" CA  ASP B 205 "
       pdb=" C   ASP B 205 "
    ideal  model  delta    sigma   weight residual
    1.523  1.507  0.017 1.80e-02 3.09e+03 8.61e-01
  bond pdb=" CB  CYS S  96 "
       pdb=" SG  CYS S  96 "
    ideal  model  delta    sigma   weight residual
    1.808  1.782  0.026 3.30e-02 9.18e+02 6.15e-01
  ... (remaining 8666 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 11583
        1.97 -     3.93: 136
        3.93 -     5.90: 22
        5.90 -     7.86: 9
        7.86 -     9.83: 1
  Bond angle restraints: 11751
  Sorted by residual:
  angle pdb=" CA  LEU R  52 "
        pdb=" CB  LEU R  52 "
        pdb=" CG  LEU R  52 "
      ideal   model   delta    sigma   weight residual
     116.30  126.13   -9.83 3.50e+00 8.16e-02 7.89e+00
  angle pdb=" N   LEU B 308 "
        pdb=" CA  LEU B 308 "
        pdb=" C   LEU B 308 "
      ideal   model   delta    sigma   weight residual
     114.04  110.76    3.28 1.24e+00 6.50e-01 6.99e+00
  angle pdb=" CA  TRP R 144 "
        pdb=" CB  TRP R 144 "
        pdb=" CG  TRP R 144 "
      ideal   model   delta    sigma   weight residual
     113.60  118.31   -4.71 1.90e+00 2.77e-01 6.15e+00
  angle pdb=" O1  PLM R 401 "
        pdb=" C1  PLM R 401 "
        pdb=" O2  PLM R 401 "
      ideal   model   delta    sigma   weight residual
     126.37  118.94    7.43 3.00e+00 1.11e-01 6.13e+00
  angle pdb=" O1  PLM R 402 "
        pdb=" C1  PLM R 402 "
        pdb=" O2  PLM R 402 "
      ideal   model   delta    sigma   weight residual
     126.37  118.95    7.42 3.00e+00 1.11e-01 6.12e+00
  ... (remaining 11746 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 4450
       17.69 -    35.38: 515
       35.38 -    53.07: 132
       53.07 -    70.76: 29
       70.76 -    88.45: 3
  Dihedral angle restraints: 5129
    sinusoidal: 1910
      harmonic: 3219
  Sorted by residual:
  dihedral pdb=" CB  CYS R 164 "
           pdb=" SG  CYS R 164 "
           pdb=" SG  CYS R 175 "
           pdb=" CB  CYS R 175 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -29.61  -56.39     1      1.00e+01 1.00e-02 4.29e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.26   18.74     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  LEU B  51 "
           pdb=" C   LEU B  51 "
           pdb=" N   ARG B  52 "
           pdb=" CA  ARG B  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.38  -18.62     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 5126 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 918
       0.032 -    0.064: 294
       0.064 -    0.096: 95
       0.096 -    0.128: 45
       0.128 -    0.160: 5
  Chirality restraints: 1357
  Sorted by residual:
  chirality pdb=" CA  ILE S 177 "
            pdb=" N   ILE S 177 "
            pdb=" C   ILE S 177 "
            pdb=" CB  ILE S 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.44e-01
  chirality pdb=" CA  ILE B 123 "
            pdb=" N   ILE B 123 "
            pdb=" C   ILE B 123 "
            pdb=" CB  ILE B 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.23e-01
  chirality pdb=" CA  TRP R 144 "
            pdb=" N   TRP R 144 "
            pdb=" C   TRP R 144 "
            pdb=" CB  TRP R 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.00e-01
  ... (remaining 1354 not shown)

  Planarity restraints: 1467
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 235 "    0.033 5.00e-02 4.00e+02   5.04e-02 4.06e+00
        pdb=" N   PRO R 236 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO R 236 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO R 236 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET R 187 "   -0.008 2.00e-02 2.50e+03   1.64e-02 2.70e+00
        pdb=" C   MET R 187 "    0.028 2.00e-02 2.50e+03
        pdb=" O   MET R 187 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLY R 188 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 230 "    0.006 2.00e-02 2.50e+03   1.29e-02 1.66e+00
        pdb=" C   PHE R 230 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   PHE R 230 "    0.008 2.00e-02 2.50e+03
        pdb=" N   LEU R 231 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1464 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1815
        2.78 -     3.31: 7720
        3.31 -     3.84: 14420
        3.84 -     4.37: 17016
        4.37 -     4.90: 29915
  Nonbonded interactions: 70886
  Sorted by model distance:
  nonbonded pdb=" O   THR R 191 "
            pdb=" OG1 THR R 195 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" NE  ARG B 283 "
            pdb=" OD1 ASP B 298 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" OD1 ASP R  72 "
            pdb=" OG  SER R 269 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OH  TYR R 109 "
            pdb=" O   SER R 234 "
     model   vdw
     2.309 3.040
  ... (remaining 70881 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     22.440
  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:11.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8671  Z= 0.170
  Angle     :  0.563   9.830  11751  Z= 0.277
  Chirality :  0.039   0.160   1357
  Planarity :  0.003   0.050   1467
  Dihedral  : 16.240  88.452   3041
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 20.22 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.26 (0.26), residues: 1093
  helix:  2.64 (0.28), residues: 374
  sheet:  0.54 (0.32), residues: 255
  loop : -0.51 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 144 
 HIS   0.008   0.001   HIS B 183 
 PHE   0.015   0.001   PHE R 202 
 TYR   0.012   0.001   TYR S 178 
 ARG   0.004   0.000   ARG S 148 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.819 
Fit side-chains
REVERT: R  159 LEU cc_start: 0.8101 (tp) cc_final: 0.7819 (tt)
  outliers start: 24
  outliers final: 21
  residues processed: 130
  average time/residue: 1.2452
  time to fit residues: 173.1062
Evaluate side-chains
  126 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   49 ILE
Chi-restraints excluded: chain R residue   81 SER
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  265 SER
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  269 SER
Chi-restraints excluded: chain S residue   23 SER
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   chunk 27 optimal weight:    0.5980
   chunk 55 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B 259 GLN
B 340 ASN
C  59 ASN
S 130 GLN
S 167 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.174999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.134948 restraints weight = 9193.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.92
r_work: 0.3290 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.0631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8671  Z= 0.186
  Angle     :  0.502   7.472  11751  Z= 0.266
  Chirality :  0.040   0.158   1357
  Planarity :  0.003   0.057   1467
  Dihedral  :  6.964  59.958   1264
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.21 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.37 (0.26), residues: 1093
  helix:  2.77 (0.27), residues: 377
  sheet:  0.64 (0.31), residues: 252
  loop : -0.51 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 144 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.014   0.001   PHE R 202 
 TYR   0.012   0.001   TYR S 178 
 ARG   0.003   0.000   ARG A 208 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 0.931 
Fit side-chains
REVERT: B  259 GLN cc_start: 0.8092 (pt0) cc_final: 0.7882 (pt0)
REVERT: R  159 LEU cc_start: 0.7899 (tp) cc_final: 0.7675 (tt)
  outliers start: 28
  outliers final: 14
  residues processed: 123
  average time/residue: 1.1912
  time to fit residues: 156.7115
Evaluate side-chains
  113 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain R residue   49 ILE
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 97 optimal weight:    9.9990
   chunk 78 optimal weight:    0.0570
   chunk 80 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 13 optimal weight:    7.9990
   chunk 70 optimal weight:    0.8980
   chunk 104 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.7702

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B  88 ASN
S 167 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.172427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.132051 restraints weight = 9296.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 2.07
r_work: 0.3214 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3084 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.0809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8671  Z= 0.282
  Angle     :  0.547   7.392  11751  Z= 0.287
  Chirality :  0.042   0.175   1357
  Planarity :  0.004   0.056   1467
  Dihedral  :  6.700  57.522   1249
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 19.66 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.26 (0.26), residues: 1093
  helix:  2.73 (0.27), residues: 377
  sheet:  0.45 (0.31), residues: 260
  loop : -0.55 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP R 144 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.015   0.002   PHE R 202 
 TYR   0.017   0.001   TYR S 178 
 ARG   0.003   0.000   ARG B 150 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 103
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: B  259 GLN cc_start: 0.8118 (pt0) cc_final: 0.7917 (pt0)
REVERT: R  159 LEU cc_start: 0.7850 (tp) cc_final: 0.7615 (tt)
REVERT: R  246 TRP cc_start: 0.7119 (OUTLIER) cc_final: 0.6016 (t60)
  outliers start: 34
  outliers final: 21
  residues processed: 126
  average time/residue: 1.1713
  time to fit residues: 157.9134
Evaluate side-chains
  122 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ARG
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain R residue   49 ILE
Chi-restraints excluded: chain R residue  175 CYS
Chi-restraints excluded: chain R residue  178 VAL
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  246 TRP
Chi-restraints excluded: chain R residue  265 SER
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 103 optimal weight:    7.9990
   chunk 102 optimal weight:    1.9990
   chunk 66 optimal weight:    0.3980
   chunk 3 optimal weight:    0.2980
   chunk 8 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 10 optimal weight:    9.9990
   chunk 101 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
S 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.175668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.136057 restraints weight = 9249.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 1.88
r_work: 0.3305 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.0862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8671  Z= 0.153
  Angle     :  0.489   8.112  11751  Z= 0.255
  Chirality :  0.039   0.152   1357
  Planarity :  0.003   0.060   1467
  Dihedral  :  6.184  56.923   1249
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 20.90 %
    Favored  : 76.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.34 (0.26), residues: 1093
  helix:  2.80 (0.27), residues: 379
  sheet:  0.52 (0.31), residues: 260
  loop : -0.54 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 144 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.015   0.001   PHE R 202 
 TYR   0.012   0.001   TYR S 178 
 ARG   0.001   0.000   ARG A 208 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7886 (m-40)
REVERT: B  259 GLN cc_start: 0.8072 (pt0) cc_final: 0.7858 (pt0)
REVERT: R   52 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7543 (tt)
REVERT: R  246 TRP cc_start: 0.7053 (OUTLIER) cc_final: 0.5970 (t60)
  outliers start: 27
  outliers final: 14
  residues processed: 122
  average time/residue: 1.1976
  time to fit residues: 156.0851
Evaluate side-chains
  115 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain R residue   49 ILE
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue  175 CYS
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  246 TRP
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
S 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.174548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.134387 restraints weight = 9161.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 1.97
r_work: 0.3276 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.0925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8671  Z= 0.201
  Angle     :  0.518  11.854  11751  Z= 0.267
  Chirality :  0.040   0.159   1357
  Planarity :  0.003   0.061   1467
  Dihedral  :  6.213  59.949   1249
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 20.79 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.37 (0.26), residues: 1093
  helix:  2.83 (0.27), residues: 378
  sheet:  0.58 (0.32), residues: 249
  loop : -0.53 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 144 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.015   0.001   PHE R 202 
 TYR   0.014   0.001   TYR S 178 
 ARG   0.002   0.000   ARG B 150 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 103
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7964 (m-40)
REVERT: B  259 GLN cc_start: 0.8088 (pt0) cc_final: 0.7869 (pt0)
REVERT: R   52 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7533 (tt)
REVERT: R  246 TRP cc_start: 0.7066 (OUTLIER) cc_final: 0.5998 (t60)
  outliers start: 31
  outliers final: 19
  residues processed: 129
  average time/residue: 1.0943
  time to fit residues: 151.4529
Evaluate side-chains
  124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain R residue   49 ILE
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue  175 CYS
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  246 TRP
Chi-restraints excluded: chain R residue  265 SER
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 27 optimal weight:    0.4980
   chunk 10 optimal weight:    0.0570
   chunk 39 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 91 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 18 optimal weight:    4.9990
   chunk 95 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 103 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
S 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.176411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.136678 restraints weight = 9197.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.90
r_work: 0.3316 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.1005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8671  Z= 0.143
  Angle     :  0.493   9.059  11751  Z= 0.253
  Chirality :  0.039   0.150   1357
  Planarity :  0.003   0.062   1467
  Dihedral  :  5.890  57.010   1249
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 21.91 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.44 (0.26), residues: 1093
  helix:  2.88 (0.27), residues: 379
  sheet:  0.65 (0.32), residues: 252
  loop : -0.52 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 144 
 HIS   0.003   0.000   HIS A 188 
 PHE   0.015   0.001   PHE R 202 
 TYR   0.011   0.001   TYR S 178 
 ARG   0.001   0.000   ARG B  49 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7983 (m-40)
REVERT: B  259 GLN cc_start: 0.8053 (pt0) cc_final: 0.7812 (pt0)
REVERT: C   21 MET cc_start: 0.7893 (mmm) cc_final: 0.7683 (mmm)
REVERT: R   52 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7445 (tt)
REVERT: R  246 TRP cc_start: 0.7025 (OUTLIER) cc_final: 0.5974 (t60)
  outliers start: 27
  outliers final: 18
  residues processed: 123
  average time/residue: 1.1538
  time to fit residues: 152.2857
Evaluate side-chains
  122 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain R residue   49 ILE
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue  175 CYS
Chi-restraints excluded: chain R residue  246 TRP
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 104 optimal weight:    3.9990
   chunk 56 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 5 optimal weight:    0.3980
   chunk 93 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 61 optimal weight:    8.9990
   chunk 72 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
S 167 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.176373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.136808 restraints weight = 9230.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 1.99
r_work: 0.3308 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8671  Z= 0.160
  Angle     :  0.497   9.060  11751  Z= 0.256
  Chirality :  0.039   0.149   1357
  Planarity :  0.003   0.063   1467
  Dihedral  :  5.736  57.399   1247
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 22.02 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.45 (0.26), residues: 1093
  helix:  2.90 (0.27), residues: 379
  sheet:  0.61 (0.32), residues: 254
  loop : -0.50 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 144 
 HIS   0.003   0.000   HIS A 188 
 PHE   0.015   0.001   PHE R 202 
 TYR   0.012   0.001   TYR S 178 
 ARG   0.001   0.000   ARG B  49 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
REVERT: B  259 GLN cc_start: 0.8062 (pt0) cc_final: 0.7823 (pt0)
REVERT: R   52 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7408 (tt)
REVERT: S   46 GLU cc_start: 0.8264 (tt0) cc_final: 0.7935 (pt0)
REVERT: S   67 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7361 (ptt90)
  outliers start: 22
  outliers final: 18
  residues processed: 121
  average time/residue: 1.1993
  time to fit residues: 155.2835
Evaluate side-chains
  121 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain R residue   49 ILE
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue  175 CYS
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 80 optimal weight:    7.9990
   chunk 66 optimal weight:    9.9990
   chunk 97 optimal weight:    3.9990
   chunk 104 optimal weight:    3.9990
   chunk 96 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0770
   chunk 82 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 15 optimal weight:   20.0000
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.3340

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
S 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.173837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.133806 restraints weight = 9308.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 2.07
r_work: 0.3235 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.1010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8671  Z= 0.231
  Angle     :  0.534   9.637  11751  Z= 0.277
  Chirality :  0.041   0.159   1357
  Planarity :  0.003   0.062   1467
  Dihedral  :  6.028  55.931   1247
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 21.80 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.39 (0.26), residues: 1093
  helix:  2.86 (0.27), residues: 379
  sheet:  0.52 (0.32), residues: 252
  loop : -0.50 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 144 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.015   0.001   PHE R 202 
 TYR   0.015   0.001   TYR S 178 
 ARG   0.002   0.000   ARG B 150 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8132 (m-40)
REVERT: R   52 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7533 (tt)
REVERT: R   79 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7205 (ttm)
REVERT: R  206 ARG cc_start: 0.7220 (tmm160) cc_final: 0.6931 (ttp-110)
REVERT: R  246 TRP cc_start: 0.7080 (OUTLIER) cc_final: 0.6033 (t60)
REVERT: S   67 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7489 (ptt90)
  outliers start: 27
  outliers final: 19
  residues processed: 130
  average time/residue: 1.3035
  time to fit residues: 180.0701
Evaluate side-chains
  127 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain R residue   49 ILE
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue   79 MET
Chi-restraints excluded: chain R residue  175 CYS
Chi-restraints excluded: chain R residue  246 TRP
Chi-restraints excluded: chain R residue  265 SER
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 102 optimal weight:    0.0050
   chunk 40 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 31 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.8998

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
S 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.175034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.134966 restraints weight = 9268.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 1.94
r_work: 0.3261 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.1089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8671  Z= 0.180
  Angle     :  0.528  10.440  11751  Z= 0.270
  Chirality :  0.040   0.162   1357
  Planarity :  0.003   0.062   1467
  Dihedral  :  5.849  56.622   1247
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.02 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.41 (0.26), residues: 1093
  helix:  2.79 (0.27), residues: 379
  sheet:  0.67 (0.32), residues: 250
  loop : -0.50 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 144 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.013   0.001   PHE A 274 
 TYR   0.012   0.001   TYR S 178 
 ARG   0.004   0.000   ARG R 103 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
REVERT: C   21 MET cc_start: 0.7856 (mmm) cc_final: 0.7626 (mmm)
REVERT: R   52 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7464 (tt)
REVERT: R   79 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7034 (ttm)
REVERT: R  206 ARG cc_start: 0.7256 (tmm160) cc_final: 0.6975 (ttp-110)
REVERT: R  246 TRP cc_start: 0.7044 (OUTLIER) cc_final: 0.6011 (t60)
REVERT: S   67 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7353 (ptt90)
  outliers start: 25
  outliers final: 17
  residues processed: 122
  average time/residue: 1.2917
  time to fit residues: 167.8698
Evaluate side-chains
  121 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain R residue   49 ILE
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue   79 MET
Chi-restraints excluded: chain R residue  175 CYS
Chi-restraints excluded: chain R residue  246 TRP
Chi-restraints excluded: chain R residue  265 SER
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 15 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0970
   chunk 94 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 102 optimal weight:    0.5980
   chunk 46 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    1.4782

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
S 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.173077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.132921 restraints weight = 9113.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 1.95
r_work: 0.3261 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8671  Z= 0.249
  Angle     :  0.576  10.031  11751  Z= 0.294
  Chirality :  0.042   0.179   1357
  Planarity :  0.003   0.062   1467
  Dihedral  :  6.118  55.659   1247
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 22.92 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.29 (0.26), residues: 1093
  helix:  2.69 (0.27), residues: 379
  sheet:  0.50 (0.32), residues: 254
  loop : -0.51 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 144 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.014   0.002   PHE R  77 
 TYR   0.016   0.001   TYR S 178 
 ARG   0.004   0.000   ARG R 103 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
REVERT: C   21 MET cc_start: 0.7922 (mmm) cc_final: 0.7692 (mmm)
REVERT: R   52 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7561 (tt)
REVERT: R  206 ARG cc_start: 0.7232 (tmm160) cc_final: 0.6954 (ttp-110)
REVERT: R  246 TRP cc_start: 0.7051 (OUTLIER) cc_final: 0.6024 (t60)
REVERT: S   67 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7567 (ptt90)
  outliers start: 24
  outliers final: 19
  residues processed: 124
  average time/residue: 1.3216
  time to fit residues: 175.1799
Evaluate side-chains
  124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain R residue   49 ILE
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue  175 CYS
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  246 TRP
Chi-restraints excluded: chain R residue  265 SER
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  129 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 89 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 83 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
S 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.175409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.135635 restraints weight = 9352.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 1.93
r_work: 0.3296 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8671  Z= 0.176
  Angle     :  0.536   9.829  11751  Z= 0.273
  Chirality :  0.040   0.167   1357
  Planarity :  0.003   0.062   1467
  Dihedral  :  5.812  56.870   1247
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 23.60 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.39 (0.26), residues: 1093
  helix:  2.75 (0.27), residues: 378
  sheet:  0.64 (0.32), residues: 255
  loop : -0.48 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 144 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.016   0.001   PHE R  77 
 TYR   0.012   0.001   TYR S 178 
 ARG   0.003   0.000   ARG R 103 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6719.92 seconds
wall clock time: 119 minutes 35.52 seconds (7175.52 seconds total)