Starting phenix.real_space_refine
on Tue Feb 11 10:47:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mk2_23884/02_2025/7mk2_23884.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mk2_23884/02_2025/7mk2_23884.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mk2_23884/02_2025/7mk2_23884.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mk2_23884/02_2025/7mk2_23884.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mk2_23884/02_2025/7mk2_23884.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mk2_23884/02_2025/7mk2_23884.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.034
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: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      34      5.16       5
     C    3390      2.51       5
     N     914      2.21       5
     O     993      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5333
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2675
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 2675
          Classifications: {'peptide': 354}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 11, 'TRANS': 342}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 80
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 57
    Chain: "B"
      Number of atoms: 2656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 2656
          Classifications: {'peptide': 354}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 11, 'TRANS': 342}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 99
          Unresolved non-hydrogen angles: 120
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 11, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 57
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    832  SG  CYS A 150     111.033  43.802  42.621  1.00 46.19           S
  ATOM    868  SG  CYS A 155     110.325  45.039  46.143  1.00 47.27           S
  ATOM    902  SG  CYS A 160     108.157  46.307  43.301  1.00 39.74           S
  ATOM   3503  SG  CYS B 150      37.143  45.391  42.094  1.00 40.69           S
  ATOM   3535  SG  CYS B 155      37.704  44.225  45.629  1.00 39.08           S
  ATOM   3569  SG  CYS B 160      39.926  42.836  42.897  1.00 40.43           S

  Time building chain proxies: 3.64, per 1000 atoms: 0.68
  Number of scatterers: 5333
  At special positions: 0
  Unit cell: (149.538, 92.2383, 62.8897, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      34     16.00
     O     993      8.00
     N     914      7.00
     C    3390      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.44
  Conformation dependent library (CDL) restraints added in 709.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" ND1 HIS A 157 "
        pdb="ZN    ZN A 701 " - pdb=" SG  CYS A 150 "
        pdb="ZN    ZN A 701 " - pdb=" SG  CYS A 160 "
        pdb="ZN    ZN A 701 " - pdb=" SG  CYS A 155 "
      pdb="  ZN B 701 "
        pdb="ZN    ZN B 701 " - pdb=" ND1 HIS B 157 "
        pdb="ZN    ZN B 701 " - pdb=" SG  CYS B 150 "
        pdb="ZN    ZN B 701 " - pdb=" SG  CYS B 155 "
        pdb="ZN    ZN B 701 " - pdb=" SG  CYS B 160 "
      Number of angles added : 6


  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1376

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 2 sheets defined
      67.2% alpha, 2.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 59
      removed outlier: 3.649A  pdb=" N   SER A  59 " --> pdb=" O   SER A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 88
      removed outlier: 3.613A  pdb=" N   LEU A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 99
    Processing helix  chain 'A' and resid 114 through 118
    Processing helix  chain 'A' and resid 125 through 138
    Processing helix  chain 'A' and resid 160 through 178
    Processing helix  chain 'A' and resid 179 through 194
    Processing helix  chain 'A' and resid 195 through 197
      No H-bonds generated for 'chain 'A' and resid 195 through 197'
    Processing helix  chain 'A' and resid 198 through 212
      removed outlier: 4.374A  pdb=" N   VAL A 204 " --> pdb=" O   GLU A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 215
      No H-bonds generated for 'chain 'A' and resid 213 through 215'
    Processing helix  chain 'A' and resid 216 through 230
      removed outlier: 3.934A  pdb=" N   ARG A 222 " --> pdb=" O   LYS A 218 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   SER A 230 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 240
      removed outlier: 3.614A  pdb=" N   LEU A 237 " --> pdb=" O   ASP A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 256
      removed outlier: 4.710A  pdb=" N   GLU A 248 " --> pdb=" O   GLU A 244 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   ASP A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ARG A 253 " --> pdb=" O   ILE A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 275
      removed outlier: 3.831A  pdb=" N   SER A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASN A 269 " --> pdb=" O   LYS A 265 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   VAL A 270 " --> pdb=" O   HIS A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 287
    Processing helix  chain 'A' and resid 292 through 297
      removed outlier: 4.126A  pdb=" N   ALA A 296 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 306
    Processing helix  chain 'A' and resid 307 through 316
      removed outlier: 3.827A  pdb=" N   LYS A 316 " --> pdb=" O   THR A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 340
      removed outlier: 3.903A  pdb=" N   LYS A 340 " --> pdb=" O   ALA A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 352
    Processing helix  chain 'A' and resid 364 through 372
      removed outlier: 3.510A  pdb=" N   ILE A 368 " --> pdb=" O   THR A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 400
      removed outlier: 3.567A  pdb=" N   CYS A 394 " --> pdb=" O   LYS A 390 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   VAL A 395 " --> pdb=" O   GLY A 391 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   GLU A 396 " --> pdb=" O   ARG A 392 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE A 397 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLN A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 59
      removed outlier: 3.719A  pdb=" N   ALA B  45 " --> pdb=" O   PRO B  41 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU B  46 " --> pdb=" O   ASP B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 87
      removed outlier: 3.711A  pdb=" N   LEU B  84 " --> pdb=" O   HIS B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 101
      removed outlier: 3.515A  pdb=" N   LYS B  92 " --> pdb=" O   SER B  88 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   LYS B 100 " --> pdb=" O   ALA B  96 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   GLU B 101 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 138
    Processing helix  chain 'B' and resid 160 through 178
    Processing helix  chain 'B' and resid 179 through 194
    Processing helix  chain 'B' and resid 198 through 212
      removed outlier: 4.707A  pdb=" N   VAL B 204 " --> pdb=" O   GLU B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 215
      No H-bonds generated for 'chain 'B' and resid 213 through 215'
    Processing helix  chain 'B' and resid 216 through 229
      removed outlier: 3.767A  pdb=" N   LYS B 229 " --> pdb=" O   GLU B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 240
      removed outlier: 3.705A  pdb=" N   SER B 240 " --> pdb=" O   SER B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 254
      removed outlier: 3.837A  pdb=" N   ARG B 252 " --> pdb=" O   GLU B 248 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   LYS B 254 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 275
      removed outlier: 3.954A  pdb=" N   ASN B 269 " --> pdb=" O   LYS B 265 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   VAL B 270 " --> pdb=" O   HIS B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 290
    Processing helix  chain 'B' and resid 292 through 296
    Processing helix  chain 'B' and resid 297 through 305
    Processing helix  chain 'B' and resid 307 through 317
    Processing helix  chain 'B' and resid 331 through 340
      removed outlier: 3.546A  pdb=" N   VAL B 335 " --> pdb=" O   THR B 331 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LYS B 340 " --> pdb=" O   ALA B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 351
    Processing helix  chain 'B' and resid 364 through 373
      removed outlier: 3.502A  pdb=" N   THR B 373 " --> pdb=" O   ALA B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 398
      removed outlier: 3.500A  pdb=" N   LEU B 393 " --> pdb=" O   LEU B 389 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL B 395 " --> pdb=" O   GLY B 391 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   GLU B 396 " --> pdb=" O   ARG B 392 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ILE B 397 " --> pdb=" O   LEU B 393 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU B 398 " --> pdb=" O   CYS B 394 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79
    Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 79
      removed outlier: 6.749A  pdb=" N   LYS B  68 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)

    280 hydrogen bonds defined for protein.
    828 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: 1.28

  Time building geometry restraints manager: 1.64 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: 1759
        1.34 -     1.46: 848
        1.46 -     1.57: 2752
        1.57 -     1.69: 0
        1.69 -     1.81: 46
  Bond restraints: 5405
  Sorted by residual:
  bond pdb=" C   VAL A 260 "
       pdb=" N   PRO A 261 "
    ideal  model  delta    sigma   weight residual
    1.334  1.369 -0.035 2.34e-02 1.83e+03 2.22e+00
  bond pdb=" CG1 ILE A 183 "
       pdb=" CD1 ILE A 183 "
    ideal  model  delta    sigma   weight residual
    1.513  1.459  0.054 3.90e-02 6.57e+02 1.91e+00
  bond pdb=" CG1 ILE B 183 "
       pdb=" CD1 ILE B 183 "
    ideal  model  delta    sigma   weight residual
    1.513  1.460  0.053 3.90e-02 6.57e+02 1.82e+00
  bond pdb=" CB  MET A 367 "
       pdb=" CG  MET A 367 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.23e+00
  bond pdb=" CB  CYS A 223 "
       pdb=" SG  CYS A 223 "
    ideal  model  delta    sigma   weight residual
    1.808  1.773  0.035 3.30e-02 9.18e+02 1.13e+00
  ... (remaining 5400 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 7049
        1.58 -     3.15: 226
        3.15 -     4.73: 33
        4.73 -     6.30: 12
        6.30 -     7.88: 1
  Bond angle restraints: 7321
  Sorted by residual:
  angle pdb=" N   VAL A 158 "
        pdb=" CA  VAL A 158 "
        pdb=" C   VAL A 158 "
      ideal   model   delta    sigma   weight residual
     113.53  110.41    3.12 9.80e-01 1.04e+00 1.01e+01
  angle pdb=" C   SER B 276 "
        pdb=" N   ASP B 277 "
        pdb=" CA  ASP B 277 "
      ideal   model   delta    sigma   weight residual
     121.54  127.46   -5.92 1.91e+00 2.74e-01 9.61e+00
  angle pdb=" C   GLU B 149 "
        pdb=" N   CYS B 150 "
        pdb=" CA  CYS B 150 "
      ideal   model   delta    sigma   weight residual
     121.54  115.97    5.57 1.91e+00 2.74e-01 8.49e+00
  angle pdb=" C   VAL B 164 "
        pdb=" N   ASP B 165 "
        pdb=" CA  ASP B 165 "
      ideal   model   delta    sigma   weight residual
     121.14  116.30    4.84 1.75e+00 3.27e-01 7.64e+00
  angle pdb=" N   VAL B 194 "
        pdb=" CA  VAL B 194 "
        pdb=" C   VAL B 194 "
      ideal   model   delta    sigma   weight residual
     109.34  114.40   -5.06 2.08e+00 2.31e-01 5.92e+00
  ... (remaining 7316 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 2984
       16.99 -    33.98: 294
       33.98 -    50.98: 61
       50.98 -    67.97: 9
       67.97 -    84.96: 3
  Dihedral angle restraints: 3351
    sinusoidal: 1255
      harmonic: 2096
  Sorted by residual:
  dihedral pdb=" CA  LYS B 119 "
           pdb=" C   LYS B 119 "
           pdb=" N   ASP B 120 "
           pdb=" CA  ASP B 120 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.59  -17.41     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CG  ARG B  87 "
           pdb=" CD  ARG B  87 "
           pdb=" NE  ARG B  87 "
           pdb=" CZ  ARG B  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.94   43.06     2      1.50e+01 4.44e-03 9.95e+00
  dihedral pdb=" CA  GLU B 149 "
           pdb=" C   GLU B 149 "
           pdb=" N   CYS B 150 "
           pdb=" CA  CYS B 150 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.29  -15.71     0      5.00e+00 4.00e-02 9.87e+00
  ... (remaining 3348 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 561
       0.036 -    0.071: 258
       0.071 -    0.107: 62
       0.107 -    0.143: 19
       0.143 -    0.178: 2
  Chirality restraints: 902
  Sorted by residual:
  chirality pdb=" CA  MET B 367 "
            pdb=" N   MET B 367 "
            pdb=" C   MET B 367 "
            pdb=" CB  MET B 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.95e-01
  chirality pdb=" CA  ASP B 277 "
            pdb=" N   ASP B 277 "
            pdb=" C   ASP B 277 "
            pdb=" CB  ASP B 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.16e-01
  chirality pdb=" CA  ASP B 165 "
            pdb=" N   ASP B 165 "
            pdb=" C   ASP B 165 "
            pdb=" CB  ASP B 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.59e-01
  ... (remaining 899 not shown)

  Planarity restraints: 924
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 141 "   -0.027 5.00e-02 4.00e+02   4.18e-02 2.79e+00
        pdb=" N   PRO B 142 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 142 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 142 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 260 "    0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO B 261 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 261 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 261 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  59 "   -0.025 5.00e-02 4.00e+02   3.71e-02 2.21e+00
        pdb=" N   PRO B  60 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B  60 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  60 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 921 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 954
        2.76 -     3.30: 5420
        3.30 -     3.83: 8140
        3.83 -     4.37: 9041
        4.37 -     4.90: 15462
  Nonbonded interactions: 39017
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 303 "
            pdb=" NH1 ARG B 339 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" OD1 ASP B 152 "
            pdb=" N   GLU B 153 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" O   ASN B 307 "
            pdb=" OG1 THR B 310 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   SER B 138 "
            pdb=" OG  SER B 138 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" NH2 ARG B 325 "
            pdb=" OE2 GLU B 357 "
     model   vdw
     2.303 3.120
  ... (remaining 39012 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 40 through 144 or (resid 145 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 146 through 152 or (resid 153 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 154 through 258 or (resid 2 \ 
59 and (name N or name CA or name C or name O or name CB )) or resid 260 through \ 
 261 or (resid 262 through 264 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 265 through 285 or (resid 286 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 287 through 350 or (resid 351 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 352 through 389 or (resid 390 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 391 through 395 \ 
 or (resid 396 and (name N or name CA or name C or name O or name CB )) or resid \ 
 397 or (resid 398 through 402 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 701))
  selection = (chain 'B' and (resid 40 through 243 or (resid 244 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 245 through 286 or (resid 287 and (name N o \ 
r name CA or name C or name O or name CB or name CG )) or resid 288 through 340  \ 
or (resid 341 and (name N or name CA or name C or name O or name CB )) or resid  \ 
342 through 399 or (resid 400 through 402 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 701))
}

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:             0.690
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.930
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
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      :  0.004   0.054   5405  Z= 0.289
  Angle     :  0.692   7.876   7321  Z= 0.381
  Chirality :  0.044   0.178    902
  Planarity :  0.004   0.042    924
  Dihedral  : 14.228  84.962   1975
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  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: -1.60 (0.32), residues: 700
  helix: -0.28 (0.26), residues: 416
  sheet:  None (None), residues: 0
  loop : -2.22 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS B 334 
 PHE   0.012   0.001   PHE B  53 
 TYR   0.011   0.002   TYR B 186 
 ARG   0.005   0.000   ARG A 363 

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.578 
Fit side-chains
REVERT: A   44 SER cc_start: 0.8001 (p) cc_final: 0.7726 (p)
REVERT: A   48 LEU cc_start: 0.8885 (mt) cc_final: 0.8294 (mt)
REVERT: A  234 MET cc_start: 0.7907 (ttp) cc_final: 0.7351 (ttm)
REVERT: A  316 LYS cc_start: 0.8262 (tmtt) cc_final: 0.7868 (tptp)
REVERT: B   51 ASN cc_start: 0.8623 (m110) cc_final: 0.8259 (m110)
REVERT: B  208 LEU cc_start: 0.9012 (tt) cc_final: 0.8727 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1396
  time to fit residues: 23.5343
Evaluate side-chains
  98 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0030
   chunk 28 optimal weight:    0.3980
   chunk 54 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 33 optimal weight:    0.1980
   chunk 40 optimal weight:    0.4980
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.3390

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

Flipped N/Q/H residues before XYZ refinement:
B 189 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.162114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.141249 restraints weight = 7016.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.144295 restraints weight = 4264.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.146516 restraints weight = 2987.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.0984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5405  Z= 0.198
  Angle     :  0.642   7.717   7321  Z= 0.331
  Chirality :  0.042   0.168    902
  Planarity :  0.004   0.040    924
  Dihedral  :  4.872  22.559    750
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.22 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.31), residues: 700
  helix: -0.22 (0.25), residues: 444
  sheet:  None (None), residues: 0
  loop : -2.09 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 290 
 PHE   0.012   0.001   PHE B  53 
 TYR   0.015   0.001   TYR B 186 
 ARG   0.002   0.000   ARG A 139 

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.577 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8746 (mt) cc_final: 0.8204 (mt)
REVERT: A  234 MET cc_start: 0.8041 (ttp) cc_final: 0.7669 (ttm)
REVERT: A  316 LYS cc_start: 0.8211 (tmtt) cc_final: 0.7722 (tptp)
REVERT: B  208 LEU cc_start: 0.8950 (tt) cc_final: 0.8696 (tt)
  outliers start: 10
  outliers final: 8
  residues processed: 120
  average time/residue: 0.1272
  time to fit residues: 21.2826
Evaluate side-chains
  112 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  227 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 68 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  51 ASN
B 187 GLN
B 189 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.159160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.138228 restraints weight = 6973.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.141291 restraints weight = 4292.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.143466 restraints weight = 3004.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.1152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   5405  Z= 0.273
  Angle     :  0.639   8.157   7321  Z= 0.333
  Chirality :  0.042   0.155    902
  Planarity :  0.004   0.046    924
  Dihedral  :  4.804  21.125    750
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.23 %
    Favored  : 81.15 %
  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: -1.42 (0.31), residues: 700
  helix: -0.25 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -2.13 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 300 
 PHE   0.012   0.001   PHE A  79 
 TYR   0.012   0.001   TYR B 186 
 ARG   0.002   0.000   ARG B 161 

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.634 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8644 (mt) cc_final: 0.8095 (mt)
REVERT: A  234 MET cc_start: 0.7904 (ttp) cc_final: 0.7201 (ttm)
REVERT: A  316 LYS cc_start: 0.8296 (tmtt) cc_final: 0.7962 (tptp)
REVERT: B   51 ASN cc_start: 0.8514 (m-40) cc_final: 0.8204 (m110)
  outliers start: 15
  outliers final: 14
  residues processed: 117
  average time/residue: 0.1345
  time to fit residues: 21.6442
Evaluate side-chains
  118 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0070
   chunk 29 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 13 optimal weight:    0.3980
   chunk 50 optimal weight:    0.0270
   chunk 68 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.3256

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

Flipped N/Q/H residues before XYZ refinement:
B 187 GLN
B 189 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.162543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.141610 restraints weight = 7139.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.144800 restraints weight = 4299.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.147063 restraints weight = 2966.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5405  Z= 0.176
  Angle     :  0.577   7.167   7321  Z= 0.299
  Chirality :  0.040   0.150    902
  Planarity :  0.004   0.044    924
  Dihedral  :  4.592  22.846    750
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 18.67 %
    Favored  : 78.36 %
  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: -1.27 (0.31), residues: 700
  helix: -0.12 (0.25), residues: 446
  sheet:  None (None), residues: 0
  loop : -2.09 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 189 
 PHE   0.010   0.001   PHE B  53 
 TYR   0.013   0.001   TYR B 186 
 ARG   0.003   0.000   ARG B 339 

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.630 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8614 (mt) cc_final: 0.8046 (mt)
REVERT: A  234 MET cc_start: 0.7864 (ttp) cc_final: 0.7205 (ttm)
REVERT: A  316 LYS cc_start: 0.8475 (tmtt) cc_final: 0.8251 (tptp)
  outliers start: 17
  outliers final: 10
  residues processed: 120
  average time/residue: 0.1191
  time to fit residues: 20.4166
Evaluate side-chains
  113 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  310 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 52 optimal weight:    0.0980
   chunk 37 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 27 optimal weight:    0.4980
   chunk 30 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 68 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0270
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
B 189 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.162197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.141161 restraints weight = 6970.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.144457 restraints weight = 4203.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.146670 restraints weight = 2881.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5405  Z= 0.193
  Angle     :  0.615   8.909   7321  Z= 0.307
  Chirality :  0.041   0.185    902
  Planarity :  0.004   0.043    924
  Dihedral  :  4.478  22.259    750
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.20 %
    Favored  : 77.31 %
  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: -1.14 (0.32), residues: 700
  helix: -0.02 (0.25), residues: 446
  sheet:  None (None), residues: 0
  loop : -2.04 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 300 
 PHE   0.015   0.001   PHE B  53 
 TYR   0.011   0.001   TYR B 186 
 ARG   0.003   0.000   ARG B 339 

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.544 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8569 (mt) cc_final: 0.8031 (mt)
REVERT: A  234 MET cc_start: 0.7897 (ttp) cc_final: 0.7211 (ttm)
REVERT: B   51 ASN cc_start: 0.8472 (m110) cc_final: 0.8208 (m110)
  outliers start: 20
  outliers final: 16
  residues processed: 112
  average time/residue: 0.1192
  time to fit residues: 19.0816
Evaluate side-chains
  114 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  335 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 8 optimal weight:    0.3980
   chunk 56 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0980
   chunk 28 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0170
   chunk 7 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 19 optimal weight:    0.1980
   overall best weight:    0.2618

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

Flipped N/Q/H residues before XYZ refinement:
B 189 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.165943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.144930 restraints weight = 7004.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.148216 restraints weight = 4211.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.150466 restraints weight = 2881.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
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   0.038   5405  Z= 0.159
  Angle     :  0.582   7.715   7321  Z= 0.292
  Chirality :  0.040   0.147    902
  Planarity :  0.003   0.039    924
  Dihedral  :  4.306  22.706    750
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.55 %
    Favored  : 77.31 %
  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: -1.00 (0.32), residues: 700
  helix:  0.09 (0.25), residues: 446
  sheet:  None (None), residues: 0
  loop : -1.97 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 189 
 PHE   0.014   0.001   PHE B  53 
 TYR   0.011   0.001   TYR B 186 
 ARG   0.002   0.000   ARG B 339 

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.641 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8527 (mt) cc_final: 0.7968 (mt)
REVERT: A   62 ASP cc_start: 0.8320 (t70) cc_final: 0.8064 (t0)
REVERT: A  234 MET cc_start: 0.7869 (ttp) cc_final: 0.7160 (ttm)
REVERT: A  393 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6308 (mm)
REVERT: B   51 ASN cc_start: 0.8520 (m110) cc_final: 0.8278 (m110)
REVERT: B  208 LEU cc_start: 0.9155 (tt) cc_final: 0.8951 (tt)
  outliers start: 18
  outliers final: 16
  residues processed: 113
  average time/residue: 0.1152
  time to fit residues: 19.0899
Evaluate side-chains
  117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 61 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0370
   chunk 20 optimal weight:    0.0770
   chunk 42 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.4016

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
B 189 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.163006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.141864 restraints weight = 6915.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.145159 restraints weight = 4160.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.147478 restraints weight = 2854.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5405  Z= 0.191
  Angle     :  0.613   9.794   7321  Z= 0.302
  Chirality :  0.040   0.138    902
  Planarity :  0.004   0.038    924
  Dihedral  :  4.270  21.868    750
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 18.50 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.32), residues: 700
  helix:  0.14 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.92 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 189 
 PHE   0.012   0.001   PHE B  53 
 TYR   0.011   0.001   TYR B 186 
 ARG   0.003   0.000   ARG B 339 

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.609 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8492 (mt) cc_final: 0.7983 (mt)
REVERT: A   62 ASP cc_start: 0.8343 (t70) cc_final: 0.8085 (t0)
REVERT: A  122 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7481 (tp30)
REVERT: A  234 MET cc_start: 0.7697 (ttp) cc_final: 0.7100 (ttm)
REVERT: A  393 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6080 (mm)
REVERT: B   51 ASN cc_start: 0.8546 (m110) cc_final: 0.8292 (m110)
REVERT: B  339 ARG cc_start: 0.8563 (tpt-90) cc_final: 0.8337 (tpt-90)
  outliers start: 22
  outliers final: 20
  residues processed: 115
  average time/residue: 0.1392
  time to fit residues: 22.0255
Evaluate side-chains
  125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  367 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 67 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0970
   chunk 60 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0070
   chunk 39 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0980
   chunk 40 optimal weight:    0.4980
   overall best weight:    0.2396

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

Flipped N/Q/H residues before XYZ refinement:
B 189 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.166295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.145411 restraints weight = 6921.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.148668 restraints weight = 4164.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.150696 restraints weight = 2860.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   5405  Z= 0.156
  Angle     :  0.590   9.124   7321  Z= 0.292
  Chirality :  0.040   0.141    902
  Planarity :  0.003   0.040    924
  Dihedral  :  4.142  22.556    750
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.02 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.32), residues: 700
  helix:  0.21 (0.26), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.89 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 189 
 PHE   0.014   0.001   PHE B  53 
 TYR   0.011   0.001   TYR B 186 
 ARG   0.002   0.000   ARG B 339 

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.628 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8521 (mt) cc_final: 0.8050 (mt)
REVERT: A   62 ASP cc_start: 0.8340 (t70) cc_final: 0.8068 (t0)
REVERT: A  122 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7464 (tp30)
REVERT: A  234 MET cc_start: 0.7767 (ttp) cc_final: 0.7137 (ttm)
REVERT: B  217 MET cc_start: 0.7006 (tpp) cc_final: 0.5479 (tpt)
  outliers start: 20
  outliers final: 18
  residues processed: 118
  average time/residue: 0.1240
  time to fit residues: 20.9557
Evaluate side-chains
  121 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0170
   chunk 62 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0980
   chunk 60 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0050
   overall best weight:    0.2632

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

Flipped N/Q/H residues before XYZ refinement:
B  51 ASN
B 189 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.165390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.144492 restraints weight = 6909.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.147785 restraints weight = 4160.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.149844 restraints weight = 2849.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5405  Z= 0.165
  Angle     :  0.612   8.486   7321  Z= 0.303
  Chirality :  0.040   0.213    902
  Planarity :  0.003   0.041    924
  Dihedral  :  4.139  22.145    750
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 19.20 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.32), residues: 700
  helix:  0.23 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.87 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 189 
 PHE   0.013   0.001   PHE B  53 
 TYR   0.010   0.001   TYR B 186 
 ARG   0.002   0.000   ARG B 339 

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.639 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8528 (mt) cc_final: 0.8035 (mt)
REVERT: A   62 ASP cc_start: 0.8342 (t70) cc_final: 0.8088 (t0)
REVERT: A   79 PHE cc_start: 0.8465 (p90) cc_final: 0.8197 (p90)
REVERT: A  122 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7478 (tp30)
REVERT: A  234 MET cc_start: 0.7777 (ttp) cc_final: 0.7141 (ttm)
REVERT: A  393 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6197 (mm)
REVERT: B   51 ASN cc_start: 0.8498 (m-40) cc_final: 0.8247 (m110)
  outliers start: 22
  outliers final: 19
  residues processed: 115
  average time/residue: 0.1174
  time to fit residues: 19.4659
Evaluate side-chains
  121 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  368 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 19 optimal weight:    0.2980
   chunk 14 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0270
   chunk 21 optimal weight:    0.0970
   chunk 37 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0670
   chunk 48 optimal weight:    0.3980
   chunk 56 optimal weight:    0.6980
   chunk 2 optimal weight:    0.2980
   overall best weight:    0.1574

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

Flipped N/Q/H residues before XYZ refinement:
B 189 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.168510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.147483 restraints weight = 6972.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.150836 restraints weight = 4161.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.153168 restraints weight = 2835.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   5405  Z= 0.146
  Angle     :  0.609  10.451   7321  Z= 0.300
  Chirality :  0.040   0.195    902
  Planarity :  0.003   0.043    924
  Dihedral  :  4.064  22.180    750
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.42 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.32), residues: 700
  helix:  0.31 (0.26), residues: 446
  sheet:  None (None), residues: 0
  loop : -1.83 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B 290 
 PHE   0.013   0.001   PHE B  53 
 TYR   0.010   0.001   TYR B 186 
 ARG   0.002   0.000   ARG B 339 

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.529 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8497 (mt) cc_final: 0.8008 (mt)
REVERT: A   62 ASP cc_start: 0.8315 (t70) cc_final: 0.8060 (t0)
REVERT: A  122 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7469 (tp30)
REVERT: A  173 LEU cc_start: 0.7332 (mt) cc_final: 0.6768 (mt)
REVERT: A  210 ASN cc_start: 0.8159 (t0) cc_final: 0.7869 (t0)
REVERT: A  234 MET cc_start: 0.7764 (ttp) cc_final: 0.7116 (ttm)
REVERT: A  393 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6231 (mm)
REVERT: B  217 MET cc_start: 0.7190 (tpp) cc_final: 0.5617 (tpt)
  outliers start: 17
  outliers final: 15
  residues processed: 112
  average time/residue: 0.1236
  time to fit residues: 19.8479
Evaluate side-chains
  118 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  368 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0670
   chunk 38 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 30 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0970
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.3516

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.165855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.144729 restraints weight = 6923.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.148062 restraints weight = 4118.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.150364 restraints weight = 2810.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5405  Z= 0.187
  Angle     :  0.644   9.755   7321  Z= 0.318
  Chirality :  0.041   0.181    902
  Planarity :  0.004   0.043    924
  Dihedral  :  4.100  21.268    750
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 20.42 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.32), residues: 700
  helix:  0.34 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.82 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 300 
 PHE   0.015   0.001   PHE B  53 
 TYR   0.010   0.001   TYR B 186 
 ARG   0.002   0.000   ARG B 339 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1832.33 seconds
wall clock time: 33 minutes 39.29 seconds (2019.29 seconds total)