Starting phenix.real_space_refine
on Tue Mar 11 16:13:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gee_29967/03_2025/8gee_29967.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gee_29967/03_2025/8gee_29967.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gee_29967/03_2025/8gee_29967.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gee_29967/03_2025/8gee_29967.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gee_29967/03_2025/8gee_29967.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gee_29967/03_2025/8gee_29967.cif"
  }
  resolution = 3.7
  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=   0.026
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      30      5.16       5
     C    4073      2.51       5
     N    1104      2.21       5
     O    1097      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6304
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 1808
          Classifications: {'peptide': 271}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 123}
          Link IDs: {'PTRANS': 6, 'TRANS': 264}
          Chain breaks: 5
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 446
          Unresolved non-hydrogen angles: 549
          Unresolved non-hydrogen dihedrals: 357
          Unresolved non-hydrogen chiralities: 27
          Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 14, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 13}
          Unresolved non-hydrogen planarities: 273
    Chain: "B"
      Number of atoms: 2216
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2216
          Classifications: {'peptide': 330}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 101}
          Link IDs: {'PTRANS': 5, 'TRANS': 324}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 322
          Unresolved non-hydrogen angles: 400
          Unresolved non-hydrogen dihedrals: 248
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 25, 'ASN:plan1': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 13}
          Unresolved non-hydrogen planarities: 227
    Chain: "G"
      Number of atoms: 299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 299
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 110
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "R"
      Number of atoms: 1965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 1965
          Classifications: {'peptide': 282}
          Incomplete info: {'truncation_to_alanine': 94}
          Link IDs: {'PTRANS': 7, 'TRANS': 274}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 310
          Unresolved non-hydrogen angles: 391
          Unresolved non-hydrogen dihedrals: 241
          Unresolved non-hydrogen chiralities: 41
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 136
    Chain: "R"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 4.37, per 1000 atoms: 0.69
  Number of scatterers: 6304
  At special positions: 0
  Unit cell: (67.84, 96.46, 126.14, 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      30     16.00
     O    1097      8.00
     N    1104      7.00
     C    4073      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.52
  Conformation dependent library (CDL) restraints added in 972.1 milliseconds
  

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1774

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 8 sheets defined
      49.7% alpha, 14.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 3.614A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 113
    Processing helix  chain 'A' and resid 160 through 169
      removed outlier: 3.921A  pdb=" N   GLU A 164 " --> pdb=" O   ARG A 160 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ARG A 165 " --> pdb=" O   ALA A 161 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU A 168 " --> pdb=" O   GLU A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 238
      removed outlier: 4.030A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.579A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.792A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 4.396A  pdb=" N   ARG A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 4.142A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 390
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'B' and resid 8 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 14 through 24
      removed outlier: 3.782A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.837A  pdb=" N   MET R  36 " --> pdb=" O   TRP R  32 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 65
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.558A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 136
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.133A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 4.034A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
      removed outlier: 3.548A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 187
    Processing helix  chain 'R' and resid 198 through 208
      removed outlier: 3.947A  pdb=" N   SER R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.786A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.773A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 322
      removed outlier: 3.812A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 322 through 327
    Processing helix  chain 'R' and resid 329 through 340
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 210
      removed outlier: 6.488A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.542A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.443A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.505A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 3.829A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.278A  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: 3.554A  pdb=" N   LEU B 210 " --> pdb=" O   GLN B 220 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.459A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 4.013A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    385 hydrogen bonds defined for protein.
    1113 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.99

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.49: 3836
        1.49 -     1.76: 2564
        1.76 -     2.03: 38
        2.03 -     2.30: 0
        2.30 -     2.57: 1
  Bond restraints: 6439
  Sorted by residual:
  bond pdb=" C   PRO A 328 "
       pdb=" N   GLU A 330 "
    ideal  model  delta    sigma   weight residual
    1.332  2.568 -1.236 1.40e-02 5.10e+03 7.79e+03
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.451 -0.054 2.00e-02 2.50e+03 7.30e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.443 -0.049 2.00e-02 2.50e+03 6.00e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.567 -0.047 2.00e-02 2.50e+03 5.43e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.568 -0.045 2.00e-02 2.50e+03 5.13e+00
  ... (remaining 6434 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.35: 8846
        9.35 -    18.71: 0
       18.71 -    28.06: 1
       28.06 -    37.41: 1
       37.41 -    46.77: 1
  Bond angle restraints: 8849
  Sorted by residual:
  angle pdb=" O   PRO A 328 "
        pdb=" C   PRO A 328 "
        pdb=" N   GLU A 330 "
      ideal   model   delta    sigma   weight residual
     122.64   86.96   35.68 1.35e+00 5.49e-01 6.98e+02
  angle pdb=" C   PRO A 328 "
        pdb=" N   GLU A 330 "
        pdb=" CA  GLU A 330 "
      ideal   model   delta    sigma   weight residual
     121.54  168.31  -46.77 1.91e+00 2.74e-01 6.00e+02
  angle pdb=" CA  PRO A 328 "
        pdb=" C   PRO A 328 "
        pdb=" N   GLU A 330 "
      ideal   model   delta    sigma   weight residual
     116.70  139.56  -22.86 2.07e+00 2.33e-01 1.22e+02
  angle pdb=" C   THR A 325 "
        pdb=" N   PRO A 326 "
        pdb=" CA  PRO A 326 "
      ideal   model   delta    sigma   weight residual
     120.51  113.81    6.70 1.26e+00 6.30e-01 2.83e+01
  angle pdb=" CA  THR A 325 "
        pdb=" C   THR A 325 "
        pdb=" N   PRO A 326 "
      ideal   model   delta    sigma   weight residual
     117.75  114.22    3.53 9.90e-01 1.02e+00 1.27e+01
  ... (remaining 8844 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 3424
       17.46 -    34.91: 213
       34.91 -    52.37: 29
       52.37 -    69.83: 3
       69.83 -    87.29: 3
  Dihedral angle restraints: 3672
    sinusoidal: 948
      harmonic: 2724
  Sorted by residual:
  dihedral pdb=" CA  PRO A 328 "
           pdb=" C   PRO A 328 "
           pdb=" N   GLU A 330 "
           pdb=" CA  GLU A 330 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  -92.71  -87.29     0      5.00e+00 4.00e-02 3.05e+02
  dihedral pdb=" CA  HIS B  54 "
           pdb=" C   HIS B  54 "
           pdb=" N   LEU B  55 "
           pdb=" CA  LEU B  55 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.32  -19.68     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.48   19.52     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 3669 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 718
       0.032 -    0.064: 242
       0.064 -    0.096: 86
       0.096 -    0.128: 32
       0.128 -    0.160: 2
  Chirality restraints: 1080
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.56   -0.16 2.00e-01 2.50e+01 6.41e-01
  chirality pdb=" CA  VAL A 214 "
            pdb=" N   VAL A 214 "
            pdb=" C   VAL A 214 "
            pdb=" CB  VAL A 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.32e-01
  chirality pdb=" CA  PRO A 326 "
            pdb=" N   PRO A 326 "
            pdb=" C   PRO A 326 "
            pdb=" CB  PRO A 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 1077 not shown)

  Planarity restraints: 1127
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 328 "   -0.116 2.00e-02 2.50e+03   1.48e-01 2.19e+02
        pdb=" C   PRO A 328 "    0.254 2.00e-02 2.50e+03
        pdb=" O   PRO A 328 "   -0.083 2.00e-02 2.50e+03
        pdb=" N   GLU A 330 "   -0.054 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 325 "    0.041 5.00e-02 4.00e+02   6.08e-02 5.92e+00
        pdb=" N   PRO A 326 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 326 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 326 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 325 "   -0.011 2.00e-02 2.50e+03   2.22e-02 4.92e+00
        pdb=" C   THR A 325 "    0.038 2.00e-02 2.50e+03
        pdb=" O   THR A 325 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   PRO A 326 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1124 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 430
        2.74 -     3.28: 6331
        3.28 -     3.82: 10731
        3.82 -     4.36: 10889
        4.36 -     4.90: 20258
  Nonbonded interactions: 48639
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN R 293 "
            pdb=" OH  TYR R 308 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OH  TYR R 185 "
            pdb=" O   PHE R 194 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OAM G1I R 501 "
     model   vdw
     2.375 3.040
  nonbonded pdb=" OD1 ASN B 295 "
            pdb=" NE  ARG B 304 "
     model   vdw
     2.402 3.120
  nonbonded pdb=" NH1 ARG B  49 "
            pdb=" O   PHE G  61 "
     model   vdw
     2.420 3.120
  ... (remaining 48634 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     18.910
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
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      :  0.016   1.236   6439  Z= 1.331
  Angle     :  0.817  46.766   8849  Z= 0.479
  Chirality :  0.039   0.160   1080
  Planarity :  0.005   0.148   1127
  Dihedral  : 12.170  87.287   1892
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.28), residues: 909
  helix:  3.01 (0.25), residues: 407
  sheet: -0.32 (0.41), residues: 163
  loop : -0.48 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP R 173 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.013   0.001   PHE B 234 
 TYR   0.011   0.001   TYR R 219 
 ARG   0.003   0.000   ARG A  42 

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.634 
Fit side-chains
REVERT: R  190 CYS cc_start: 0.7085 (t) cc_final: 0.6786 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1786
  time to fit residues: 21.9997
Evaluate side-chains
  71 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0870
   chunk 72 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.111218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.094532 restraints weight = 12525.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.096839 restraints weight = 7374.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.098356 restraints weight = 5072.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.0897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6439  Z= 0.191
  Angle     :  0.451   5.341   8849  Z= 0.253
  Chirality :  0.040   0.152   1080
  Planarity :  0.003   0.030   1127
  Dihedral  :  3.892  18.444    990
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.65 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 10.99 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.28), residues: 911
  helix:  2.94 (0.25), residues: 424
  sheet: -0.22 (0.41), residues: 163
  loop : -0.67 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP R 173 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.020   0.001   PHE A 222 
 TYR   0.009   0.001   TYR R 308 
 ARG   0.003   0.000   ARG A 385 

*********************** 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
  81 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.659 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8068 (tmm) cc_final: 0.7086 (ttp)
REVERT: R  190 CYS cc_start: 0.7099 (t) cc_final: 0.6794 (t)
  outliers start: 7
  outliers final: 5
  residues processed: 79
  average time/residue: 0.1420
  time to fit residues: 16.4237
Evaluate side-chains
  73 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.109481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.092729 restraints weight = 12657.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.095001 restraints weight = 7459.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.096432 restraints weight = 5124.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6439  Z= 0.236
  Angle     :  0.455   5.392   8849  Z= 0.254
  Chirality :  0.040   0.145   1080
  Planarity :  0.003   0.027   1127
  Dihedral  :  3.915  20.174    990
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.87 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.28), residues: 911
  helix:  3.01 (0.25), residues: 417
  sheet: -0.25 (0.41), residues: 163
  loop : -0.69 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 173 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.013   0.001   PHE B 234 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.006   0.001   ARG A  42 

*********************** 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
  78 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.665 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8029 (tmm) cc_final: 0.7156 (ttp)
REVERT: R  190 CYS cc_start: 0.7122 (t) cc_final: 0.6831 (t)
  outliers start: 9
  outliers final: 7
  residues processed: 77
  average time/residue: 0.1416
  time to fit residues: 15.9709
Evaluate side-chains
  74 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 72 optimal weight:    0.1980
   chunk 31 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 90 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.110271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.093439 restraints weight = 12682.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.095743 restraints weight = 7489.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.097217 restraints weight = 5137.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6439  Z= 0.179
  Angle     :  0.420   5.242   8849  Z= 0.236
  Chirality :  0.039   0.134   1080
  Planarity :  0.003   0.026   1127
  Dihedral  :  3.767  19.569    990
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 16.59 %
    Favored  : 80.17 %
  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:  1.71 (0.29), residues: 911
  helix:  3.01 (0.25), residues: 423
  sheet: -0.32 (0.40), residues: 163
  loop : -0.67 (0.33), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.009   0.001   PHE R 289 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.004   0.000   ARG A  42 

*********************** 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
  86 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.707 
Fit side-chains
REVERT: B  111 TYR cc_start: 0.8181 (m-80) cc_final: 0.7954 (m-80)
REVERT: R   82 MET cc_start: 0.7977 (tmm) cc_final: 0.7035 (ttp)
REVERT: R  190 CYS cc_start: 0.7106 (t) cc_final: 0.6815 (t)
  outliers start: 15
  outliers final: 12
  residues processed: 83
  average time/residue: 0.1468
  time to fit residues: 17.9738
Evaluate side-chains
  78 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  203 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 142 HIS
B 237 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.106732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.089960 restraints weight = 12857.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.092106 restraints weight = 7720.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.093474 restraints weight = 5389.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6439  Z= 0.323
  Angle     :  0.500   5.553   8849  Z= 0.277
  Chirality :  0.041   0.129   1080
  Planarity :  0.003   0.030   1127
  Dihedral  :  4.078  23.613    990
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 18.10 %
    Favored  : 77.37 %
  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:  1.50 (0.28), residues: 911
  helix:  2.87 (0.25), residues: 423
  sheet: -0.60 (0.39), residues: 167
  loop : -0.69 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 313 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.013   0.001   PHE R 289 
 TYR   0.017   0.002   TYR R 174 
 ARG   0.003   0.000   ARG A  42 

*********************** 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
  85 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.662 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8111 (tmm) cc_final: 0.7120 (ttp)
REVERT: R  190 CYS cc_start: 0.7206 (t) cc_final: 0.6922 (t)
  outliers start: 21
  outliers final: 15
  residues processed: 82
  average time/residue: 0.1340
  time to fit residues: 16.1938
Evaluate side-chains
  78 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  183 ASN
Chi-restraints excluded: chain R residue  203 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0770
   chunk 11 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.109528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.092748 restraints weight = 12617.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.095021 restraints weight = 7403.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.096452 restraints weight = 5108.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6439  Z= 0.163
  Angle     :  0.429   6.865   8849  Z= 0.237
  Chirality :  0.039   0.134   1080
  Planarity :  0.003   0.029   1127
  Dihedral  :  3.804  21.915    990
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.61 %
    Favored  : 76.94 %
  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:  1.66 (0.29), residues: 911
  helix:  3.03 (0.25), residues: 421
  sheet: -0.42 (0.40), residues: 166
  loop : -0.70 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 313 
 HIS   0.001   0.000   HIS B  54 
 PHE   0.018   0.001   PHE A 222 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.003   0.000   ARG A  42 

*********************** 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
  90 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.654 
Fit side-chains
REVERT: B  111 TYR cc_start: 0.8191 (m-80) cc_final: 0.7950 (m-80)
REVERT: R   82 MET cc_start: 0.8003 (tmm) cc_final: 0.7039 (ttp)
REVERT: R  190 CYS cc_start: 0.7122 (t) cc_final: 0.6815 (t)
  outliers start: 16
  outliers final: 10
  residues processed: 89
  average time/residue: 0.1326
  time to fit residues: 17.4127
Evaluate side-chains
  83 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 83 optimal weight:    0.0770
   chunk 49 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0370
   chunk 69 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    0.4616

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 237 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.110685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.093931 restraints weight = 12530.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.096180 restraints weight = 7413.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.097753 restraints weight = 5124.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6439  Z= 0.140
  Angle     :  0.427   6.020   8849  Z= 0.236
  Chirality :  0.039   0.132   1080
  Planarity :  0.003   0.026   1127
  Dihedral  :  3.678  19.291    990
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 21.12 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.29), residues: 911
  helix:  3.05 (0.25), residues: 421
  sheet: -0.42 (0.39), residues: 168
  loop : -0.69 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 169 
 HIS   0.002   0.000   HIS B 225 
 PHE   0.018   0.001   PHE A 222 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.003   0.000   ARG B 251 

*********************** 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
  88 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
REVERT: R   82 MET cc_start: 0.7941 (tmm) cc_final: 0.7039 (ttp)
  outliers start: 12
  outliers final: 10
  residues processed: 85
  average time/residue: 0.1450
  time to fit residues: 17.8398
Evaluate side-chains
  78 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 64 optimal weight:    0.0040
   chunk 60 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0170
   chunk 14 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.4230

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 294 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.111445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.094263 restraints weight = 12589.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.096580 restraints weight = 7407.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.098200 restraints weight = 5097.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6439  Z= 0.132
  Angle     :  0.423   5.805   8849  Z= 0.232
  Chirality :  0.039   0.131   1080
  Planarity :  0.002   0.026   1127
  Dihedral  :  3.622  16.960    990
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 21.34 %
    Favored  : 75.65 %
  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:  1.75 (0.29), residues: 911
  helix:  3.08 (0.25), residues: 423
  sheet: -0.38 (0.40), residues: 163
  loop : -0.64 (0.33), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.001   0.000   HIS A 220 
 PHE   0.023   0.001   PHE A 222 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.003   0.000   ARG A  42 

*********************** 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
  90 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.701 
Fit side-chains
REVERT: B  169 TRP cc_start: 0.8876 (m100) cc_final: 0.8083 (m100)
REVERT: R   82 MET cc_start: 0.7935 (tmm) cc_final: 0.7048 (ttp)
REVERT: R   86 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8852 (p)
REVERT: R  190 CYS cc_start: 0.7103 (t) cc_final: 0.6821 (t)
  outliers start: 14
  outliers final: 11
  residues processed: 88
  average time/residue: 0.1402
  time to fit residues: 18.2022
Evaluate side-chains
  83 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 73 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0070
   chunk 8 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0980
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.4198

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.112417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.095396 restraints weight = 12518.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.097725 restraints weight = 7335.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.099359 restraints weight = 5018.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6439  Z= 0.137
  Angle     :  0.430   6.479   8849  Z= 0.236
  Chirality :  0.040   0.153   1080
  Planarity :  0.002   0.025   1127
  Dihedral  :  3.584  16.498    990
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 21.98 %
    Favored  : 75.22 %
  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:  1.82 (0.29), residues: 911
  helix:  3.09 (0.25), residues: 423
  sheet: -0.38 (0.40), residues: 169
  loop : -0.51 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  99 
 HIS   0.002   0.000   HIS B 142 
 PHE   0.013   0.001   PHE A 222 
 TYR   0.017   0.001   TYR R 174 
 ARG   0.003   0.000   ARG A  42 

*********************** 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
  89 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.760 
Fit side-chains
REVERT: B  169 TRP cc_start: 0.8840 (m100) cc_final: 0.8035 (m100)
REVERT: R   82 MET cc_start: 0.7955 (tmm) cc_final: 0.7069 (ttp)
REVERT: R   86 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8844 (p)
REVERT: R  190 CYS cc_start: 0.7086 (t) cc_final: 0.6805 (t)
  outliers start: 13
  outliers final: 11
  residues processed: 87
  average time/residue: 0.1439
  time to fit residues: 18.4321
Evaluate side-chains
  86 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  321 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 35 optimal weight:    0.0170
   chunk 15 optimal weight:    0.4980
   chunk 28 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 7 optimal weight:   20.0000
   chunk 64 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    0.3980
   chunk 40 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0370
   overall best weight:    0.3496

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

Flipped N/Q/H residues before XYZ refinement:
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.113052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.096013 restraints weight = 12466.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.098417 restraints weight = 7256.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.100029 restraints weight = 4928.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6439  Z= 0.127
  Angle     :  0.426   6.439   8849  Z= 0.232
  Chirality :  0.039   0.147   1080
  Planarity :  0.002   0.025   1127
  Dihedral  :  3.549  16.508    990
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 22.41 %
    Favored  : 75.22 %
  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:  1.86 (0.29), residues: 911
  helix:  3.14 (0.25), residues: 422
  sheet: -0.34 (0.41), residues: 168
  loop : -0.51 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 277 
 HIS   0.002   0.000   HIS A 357 
 PHE   0.036   0.001   PHE A 222 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.003   0.000   ARG A  42 

********************** 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
  84 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.737 
Fit side-chains
REVERT: A  222 PHE cc_start: 0.7645 (m-10) cc_final: 0.7382 (m-10)
REVERT: B  169 TRP cc_start: 0.8811 (m100) cc_final: 0.8000 (m100)
REVERT: R   82 MET cc_start: 0.7946 (tmm) cc_final: 0.7079 (ttp)
REVERT: R  190 CYS cc_start: 0.7070 (t) cc_final: 0.6783 (t)
  outliers start: 11
  outliers final: 8
  residues processed: 84
  average time/residue: 0.1398
  time to fit residues: 17.2702
Evaluate side-chains
  81 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 6 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 88 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.110720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.093640 restraints weight = 12824.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.095946 restraints weight = 7504.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.097571 restraints weight = 5141.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6439  Z= 0.199
  Angle     :  0.454   6.585   8849  Z= 0.248
  Chirality :  0.040   0.155   1080
  Planarity :  0.003   0.027   1127
  Dihedral  :  3.685  17.367    990
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 22.20 %
    Favored  : 75.43 %
  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:  1.81 (0.29), residues: 911
  helix:  3.07 (0.25), residues: 423
  sheet: -0.44 (0.40), residues: 169
  loop : -0.46 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B  99 
 HIS   0.002   0.001   HIS B 225 
 PHE   0.049   0.001   PHE A 222 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.002   0.000   ARG A  42 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2061.91 seconds
wall clock time: 36 minutes 26.73 seconds (2186.73 seconds total)