Starting phenix.real_space_refine
on Sun May 11 00:23:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jpp_36486/05_2025/8jpp_36486.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jpp_36486/05_2025/8jpp_36486.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jpp_36486/05_2025/8jpp_36486.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jpp_36486/05_2025/8jpp_36486.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jpp_36486/05_2025/8jpp_36486.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jpp_36486/05_2025/8jpp_36486.cif"
  }
  resolution = 3.2
  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=  -0.002 sd=   0.047
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      41      5.16       5
     C    4565      2.51       5
     N    1228      2.21       5
     O    1303      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7137
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1897
          Classifications: {'peptide': 237}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 6, 'TRANS': 230}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 41
    Chain: "B"
      Number of atoms: 2511
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2511
          Classifications: {'peptide': 331}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "G"
      Number of atoms: 376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 376
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 44}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "R"
      Number of atoms: 2345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2345
          Classifications: {'peptide': 305}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 12, 'TRANS': 292}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 154
          Unresolved non-hydrogen angles: 187
          Unresolved non-hydrogen dihedrals: 130
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 81
    Chain: "R"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SIN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.04, per 1000 atoms: 0.71
  Number of scatterers: 7137
  At special positions: 0
  Unit cell: (74.048, 99.84, 132.288, 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      41     16.00
     O    1303      8.00
     N    1228      7.00
     C    4565      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  11 " - pdb=" SG  CYS R 268 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  95 " - pdb=" SG  CYS R 172 " 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: 1.75
  Conformation dependent library (CDL) restraints added in 936.7 milliseconds
  

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1748

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 8 sheets defined
      47.0% alpha, 16.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
      removed outlier: 3.591A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 233 through 241
      removed outlier: 4.477A  pdb=" N   ASP A 240 " --> pdb=" O   CYS A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 268
    Processing helix  chain 'A' and resid 283 through 293
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 4.024A  pdb=" N   TYR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 306
    Processing helix  chain 'A' and resid 321 through 341
    Processing helix  chain 'A' and resid 360 through 381
    Processing helix  chain 'B' and resid 11 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 15 through 24
      removed outlier: 3.742A  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 11 through 50
      removed outlier: 4.260A  pdb=" N   LEU R  26 " --> pdb=" O   GLU R  22 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   SER R  27 " --> pdb=" O   LYS R  23 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LEU R  39 " --> pdb=" O   VAL R  35 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 56 through 75
      removed outlier: 3.507A  pdb=" N   THR R  75 " --> pdb=" O   ALA R  71 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 75 through 86
      removed outlier: 4.541A  pdb=" N   LEU R  79 " --> pdb=" O   THR R  75 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 90 through 126
      removed outlier: 4.173A  pdb=" N   LEU R  94 " --> pdb=" O   TYR R  90 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   CYS R  95 " --> pdb=" O   GLY R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 135 through 154
    Processing helix  chain 'R' and resid 157 through 162
    Processing helix  chain 'R' and resid 180 through 196
      removed outlier: 3.510A  pdb=" N   TYR R 187 " --> pdb=" O   TYR R 183 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 196 through 221
    Processing helix  chain 'R' and resid 227 through 258
      removed outlier: 3.560A  pdb=" N   LEU R 231 " --> pdb=" O   LEU R 227 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   PHE R 241 " --> pdb=" O   ALA R 237 " (cutoff:3.500A)
      Proline residue:  R 247  - end of helix
      removed outlier: 3.582A  pdb=" N   VAL R 254 " --> pdb=" O   VAL R 250 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 266 through 285
      removed outlier: 3.558A  pdb=" N   THR R 280 " --> pdb=" O   PHE R 276 " (cutoff:3.500A)
      Proline residue:  R 282  - end of helix
    Processing helix  chain 'R' and resid 286 through 296
      Proline residue:  R 292  - end of helix
    Processing helix  chain 'R' and resid 301 through 317
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.525A  pdb=" N   LEU A  45 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.216A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ASN A 282 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 50
      removed outlier: 6.841A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.612A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 6.278A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.317A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.584A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   MET B 217 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232
      removed outlier: 6.572A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.720A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    390 hydrogen bonds defined for protein.
    1131 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.06

  Time building geometry restraints manager: 1.99 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1162
        1.32 -     1.44: 2021
        1.44 -     1.56: 4049
        1.56 -     1.69: 0
        1.69 -     1.81: 57
  Bond restraints: 7289
  Sorted by residual:
  bond pdb=" C   LEU R 185 "
       pdb=" O   LEU R 185 "
    ideal  model  delta    sigma   weight residual
    1.234  1.195  0.040 1.17e-02 7.31e+03 1.17e+01
  bond pdb=" C   PRO R 181 "
       pdb=" O   PRO R 181 "
    ideal  model  delta    sigma   weight residual
    1.237  1.199  0.038 1.29e-02 6.01e+03 8.54e+00
  bond pdb=" N   ILE R 118 "
       pdb=" CA  ILE R 118 "
    ideal  model  delta    sigma   weight residual
    1.458  1.498 -0.040 1.41e-02 5.03e+03 8.10e+00
  bond pdb=" CA  SER A 250 "
       pdb=" CB  SER A 250 "
    ideal  model  delta    sigma   weight residual
    1.530  1.482  0.048 1.75e-02 3.27e+03 7.61e+00
  bond pdb=" N   ILE R  89 "
       pdb=" CA  ILE R  89 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.25e-02 6.40e+03 7.03e+00
  ... (remaining 7284 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 9535
        1.55 -     3.11: 306
        3.11 -     4.66: 60
        4.66 -     6.21: 9
        6.21 -     7.76: 3
  Bond angle restraints: 9913
  Sorted by residual:
  angle pdb=" N   LEU A 262 "
        pdb=" CA  LEU A 262 "
        pdb=" C   LEU A 262 "
      ideal   model   delta    sigma   weight residual
     112.23  104.47    7.76 1.26e+00 6.30e-01 3.80e+01
  angle pdb=" N   ASN R 184 "
        pdb=" CA  ASN R 184 "
        pdb=" C   ASN R 184 "
      ideal   model   delta    sigma   weight residual
     113.18  106.47    6.71 1.21e+00 6.83e-01 3.08e+01
  angle pdb=" N   ARG R 120 "
        pdb=" CA  ARG R 120 "
        pdb=" C   ARG R 120 "
      ideal   model   delta    sigma   weight residual
     112.23  106.54    5.69 1.26e+00 6.30e-01 2.04e+01
  angle pdb=" CA  PHE A 208 "
        pdb=" CB  PHE A 208 "
        pdb=" CG  PHE A 208 "
      ideal   model   delta    sigma   weight residual
     113.80  117.96   -4.16 1.00e+00 1.00e+00 1.73e+01
  angle pdb=" N   LEU A 260 "
        pdb=" CA  LEU A 260 "
        pdb=" C   LEU A 260 "
      ideal   model   delta    sigma   weight residual
     112.54  107.55    4.99 1.22e+00 6.72e-01 1.68e+01
  ... (remaining 9908 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.36: 3801
       17.36 -    34.71: 388
       34.71 -    52.06: 99
       52.06 -    69.42: 10
       69.42 -    86.77: 8
  Dihedral angle restraints: 4306
    sinusoidal: 1606
      harmonic: 2700
  Sorted by residual:
  dihedral pdb=" CD  ARG A  61 "
           pdb=" NE  ARG A  61 "
           pdb=" CZ  ARG A  61 "
           pdb=" NH1 ARG A  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -28.40   28.40     1      1.00e+01 1.00e-02 1.16e+01
  dihedral pdb=" CA  ASP R 119 "
           pdb=" CB  ASP R 119 "
           pdb=" CG  ASP R 119 "
           pdb=" OD1 ASP R 119 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.50   55.50     1      2.00e+01 2.50e-03 1.04e+01
  dihedral pdb=" CG  ARG R 303 "
           pdb=" CD  ARG R 303 "
           pdb=" NE  ARG R 303 "
           pdb=" CZ  ARG R 303 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.94   43.94     2      1.50e+01 4.44e-03 1.03e+01
  ... (remaining 4303 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 822
       0.038 -    0.076: 206
       0.076 -    0.114: 81
       0.114 -    0.152: 27
       0.152 -    0.190: 3
  Chirality restraints: 1139
  Sorted by residual:
  chirality pdb=" CA  ILE R 186 "
            pdb=" N   ILE R 186 "
            pdb=" C   ILE R 186 "
            pdb=" CB  ILE R 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.03e-01
  chirality pdb=" CB  VAL R  38 "
            pdb=" CA  VAL R  38 "
            pdb=" CG1 VAL R  38 "
            pdb=" CG2 VAL R  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.30e-01
  chirality pdb=" CA  ILE R  89 "
            pdb=" N   ILE R  89 "
            pdb=" C   ILE R  89 "
            pdb=" CB  ILE R  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.66e-01
  ... (remaining 1136 not shown)

  Planarity restraints: 1265
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  61 "   -0.519 9.50e-02 1.11e+02   2.33e-01 3.30e+01
        pdb=" NE  ARG A  61 "    0.030 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  61 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  61 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  61 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R 120 "    0.260 9.50e-02 1.11e+02   1.17e-01 8.34e+00
        pdb=" NE  ARG R 120 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG R 120 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG R 120 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG R 120 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 232 "   -0.009 2.00e-02 2.50e+03   1.80e-02 3.24e+00
        pdb=" C   ILE B 232 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ILE B 232 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   CYS B 233 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1262 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1255
        2.76 -     3.29: 7449
        3.29 -     3.83: 12170
        3.83 -     4.36: 14863
        4.36 -     4.90: 25806
  Nonbonded interactions: 61543
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" N   GLU G  47 "
            pdb=" OE1 GLU G  47 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" O   LEU R  39 "
            pdb=" OG1 THR R  42 "
     model   vdw
     2.257 3.040
  ... (remaining 61538 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.100
  Find NCS groups from input model:        0.080
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
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   0.048   7291  Z= 0.233
  Angle     :  0.652   7.764   9917  Z= 0.418
  Chirality :  0.043   0.190   1139
  Planarity :  0.008   0.233   1265
  Dihedral  : 15.093  86.773   2552
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 16.01 %
    Favored  : 83.31 %
  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: -0.08 (0.29), residues: 910
  helix:  1.32 (0.28), residues: 407
  sheet: -1.88 (0.35), residues: 173
  loop : -0.60 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 263 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.025   0.002   PHE A 208 
 TYR   0.012   0.001   TYR R 107 
 ARG   0.009   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17445 (  390)
  hydrogen bonds       : angle       7.34456 ( 1131)
  SS BOND              : bond        0.00334 (    2)
  SS BOND              : angle       0.62662 (    4)
  covalent geometry    : bond        0.00390 ( 7289)
  covalent geometry    : angle       0.65238 ( 9913)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 145
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 ARG cc_start: 0.7411 (mpt180) cc_final: 0.6551 (mtm-85)
REVERT: A   21 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7157 (tm-30)
REVERT: A  220 HIS cc_start: 0.7716 (t-170) cc_final: 0.6985 (t-170)
REVERT: A  376 MET cc_start: 0.7941 (ttm) cc_final: 0.7645 (ttt)
REVERT: B  292 PHE cc_start: 0.8634 (m-10) cc_final: 0.8272 (m-80)
REVERT: B  329 THR cc_start: 0.9005 (m) cc_final: 0.8545 (p)
  outliers start: 5
  outliers final: 2
  residues processed: 149
  average time/residue: 0.2262
  time to fit residues: 43.3418
Evaluate side-chains
  123 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 121
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0070
   chunk 37 optimal weight:    0.8980
   chunk 23 optimal weight:    9.9990
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 52 optimal weight:   10.0000
   chunk 81 optimal weight:    3.9990
   overall best weight:    0.7600

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
R 270 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.163033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.127252 restraints weight = 9353.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.70
r_work: 0.3453 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.1205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7291  Z= 0.165
  Angle     :  0.576   6.951   9917  Z= 0.304
  Chirality :  0.045   0.208   1139
  Planarity :  0.004   0.037   1265
  Dihedral  :  4.949  50.056   1012
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 14.11 %
    Favored  : 82.23 %
  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:  0.28 (0.28), residues: 910
  helix:  1.73 (0.26), residues: 406
  sheet: -1.77 (0.35), residues: 171
  loop : -0.54 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 263 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.024   0.001   TYR R 187 
 ARG   0.006   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04714 (  390)
  hydrogen bonds       : angle       4.87034 ( 1131)
  SS BOND              : bond        0.00384 (    2)
  SS BOND              : angle       0.62293 (    4)
  covalent geometry    : bond        0.00380 ( 7289)
  covalent geometry    : angle       0.57561 ( 9913)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  292 PHE cc_start: 0.8802 (m-10) cc_final: 0.8483 (m-80)
REVERT: R   33 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7962 (mt-10)
REVERT: R   41 ASN cc_start: 0.8611 (m-40) cc_final: 0.8290 (m110)
REVERT: R  186 ILE cc_start: 0.8051 (pt) cc_final: 0.7812 (mm)
  outliers start: 27
  outliers final: 15
  residues processed: 148
  average time/residue: 0.2008
  time to fit residues: 39.2003
Evaluate side-chains
  125 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   59 GLN
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   73 LEU
Chi-restraints excluded: chain R residue  114 THR
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  125 LYS
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  243 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
R  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.163379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.126985 restraints weight = 9314.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.81
r_work: 0.3443 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7291  Z= 0.163
  Angle     :  0.552   5.878   9917  Z= 0.290
  Chirality :  0.044   0.205   1139
  Planarity :  0.004   0.035   1265
  Dihedral  :  4.476  50.928   1008
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 16.15 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.28), residues: 910
  helix:  1.88 (0.26), residues: 406
  sheet: -1.72 (0.35), residues: 173
  loop : -0.57 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 263 
 HIS   0.003   0.001   HIS R 131 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.017   0.001   TYR R 187 
 ARG   0.004   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04441 (  390)
  hydrogen bonds       : angle       4.64069 ( 1131)
  SS BOND              : bond        0.00419 (    2)
  SS BOND              : angle       0.64213 (    4)
  covalent geometry    : bond        0.00380 ( 7289)
  covalent geometry    : angle       0.55192 ( 9913)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 122
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  292 PHE cc_start: 0.8818 (m-10) cc_final: 0.8566 (m-80)
REVERT: B  329 THR cc_start: 0.9092 (m) cc_final: 0.8673 (p)
REVERT: R   33 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7980 (mt-10)
REVERT: R   41 ASN cc_start: 0.8490 (m-40) cc_final: 0.8153 (m110)
  outliers start: 30
  outliers final: 20
  residues processed: 139
  average time/residue: 0.1799
  time to fit residues: 33.7037
Evaluate side-chains
  136 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain R residue   73 LEU
Chi-restraints excluded: chain R residue  114 THR
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  203 MET
Chi-restraints excluded: chain R residue  204 CYS
Chi-restraints excluded: chain R residue  243 VAL
Chi-restraints excluded: chain R residue  250 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
B 230 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.163250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.127960 restraints weight = 9469.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 2.58
r_work: 0.3449 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7291  Z= 0.159
  Angle     :  0.545   7.583   9917  Z= 0.287
  Chirality :  0.044   0.200   1139
  Planarity :  0.004   0.040   1265
  Dihedral  :  4.449  51.690   1008
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 17.37 %
    Favored  : 78.70 %
  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:  0.46 (0.28), residues: 910
  helix:  1.99 (0.26), residues: 406
  sheet: -1.76 (0.36), residues: 173
  loop : -0.57 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 263 
 HIS   0.003   0.001   HIS R 131 
 PHE   0.016   0.001   PHE A 222 
 TYR   0.019   0.001   TYR R 187 
 ARG   0.004   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04253 (  390)
  hydrogen bonds       : angle       4.52041 ( 1131)
  SS BOND              : bond        0.00423 (    2)
  SS BOND              : angle       0.58832 (    4)
  covalent geometry    : bond        0.00371 ( 7289)
  covalent geometry    : angle       0.54533 ( 9913)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  262 MET cc_start: 0.8159 (tpp) cc_final: 0.7555 (mmt)
REVERT: B  329 THR cc_start: 0.9103 (m) cc_final: 0.8686 (p)
REVERT: R   33 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8118 (mt-10)
REVERT: R   41 ASN cc_start: 0.8435 (m-40) cc_final: 0.8113 (m110)
  outliers start: 29
  outliers final: 19
  residues processed: 140
  average time/residue: 0.2135
  time to fit residues: 39.6496
Evaluate side-chains
  134 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain R residue   73 LEU
Chi-restraints excluded: chain R residue  114 THR
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  203 MET
Chi-restraints excluded: chain R residue  204 CYS
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  243 VAL
Chi-restraints excluded: chain R residue  250 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 78 optimal weight:    0.0770
   chunk 62 optimal weight:    0.8980
   chunk 12 optimal weight:    0.2980
   chunk 39 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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 = 0.4062 r_free = 0.4062 target = 0.164459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.128951 restraints weight = 9375.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 2.66
r_work: 0.3471 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7291  Z= 0.130
  Angle     :  0.521   5.889   9917  Z= 0.274
  Chirality :  0.043   0.192   1139
  Planarity :  0.004   0.038   1265
  Dihedral  :  4.386  53.562   1008
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 18.32 %
    Favored  : 77.88 %
  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:  0.55 (0.29), residues: 910
  helix:  2.11 (0.26), residues: 406
  sheet: -1.76 (0.36), residues: 173
  loop : -0.56 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 263 
 HIS   0.002   0.001   HIS A 347 
 PHE   0.014   0.001   PHE R 294 
 TYR   0.019   0.001   TYR R 187 
 ARG   0.006   0.000   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04025 (  390)
  hydrogen bonds       : angle       4.40784 ( 1131)
  SS BOND              : bond        0.00307 (    2)
  SS BOND              : angle       0.52300 (    4)
  covalent geometry    : bond        0.00292 ( 7289)
  covalent geometry    : angle       0.52067 ( 9913)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  198 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8454 (pp)
REVERT: B  246 ASP cc_start: 0.8290 (m-30) cc_final: 0.8075 (m-30)
REVERT: B  262 MET cc_start: 0.8155 (tpp) cc_final: 0.7522 (mmt)
REVERT: B  292 PHE cc_start: 0.8586 (m-80) cc_final: 0.8223 (m-80)
REVERT: B  329 THR cc_start: 0.9084 (m) cc_final: 0.8699 (p)
REVERT: R   33 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8121 (mt-10)
REVERT: R   41 ASN cc_start: 0.8338 (m-40) cc_final: 0.8029 (m110)
REVERT: R  125 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8387 (tttp)
  outliers start: 28
  outliers final: 19
  residues processed: 137
  average time/residue: 0.1909
  time to fit residues: 34.9763
Evaluate side-chains
  136 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLN
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain R residue   73 LEU
Chi-restraints excluded: chain R residue  114 THR
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  125 LYS
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  203 MET
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  243 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4053 r_free = 0.4053 target = 0.163595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.127652 restraints weight = 9306.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 2.76
r_work: 0.3452 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7291  Z= 0.156
  Angle     :  0.533   5.933   9917  Z= 0.279
  Chirality :  0.043   0.200   1139
  Planarity :  0.004   0.037   1265
  Dihedral  :  4.418  54.296   1008
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 19.40 %
    Favored  : 76.53 %
  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:  0.55 (0.29), residues: 910
  helix:  2.05 (0.26), residues: 411
  sheet: -1.80 (0.36), residues: 172
  loop : -0.49 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 263 
 HIS   0.002   0.001   HIS R 131 
 PHE   0.017   0.001   PHE A 222 
 TYR   0.017   0.001   TYR R 187 
 ARG   0.006   0.000   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04117 (  390)
  hydrogen bonds       : angle       4.41259 ( 1131)
  SS BOND              : bond        0.00409 (    2)
  SS BOND              : angle       0.49273 (    4)
  covalent geometry    : bond        0.00362 ( 7289)
  covalent geometry    : angle       0.53298 ( 9913)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 118
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
REVERT: A  220 HIS cc_start: 0.7850 (t-170) cc_final: 0.6908 (t-170)
REVERT: B  198 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8469 (pp)
REVERT: B  262 MET cc_start: 0.8154 (tpp) cc_final: 0.7518 (mmt)
REVERT: B  292 PHE cc_start: 0.8623 (m-80) cc_final: 0.8307 (m-80)
REVERT: B  329 THR cc_start: 0.9114 (m) cc_final: 0.8704 (p)
REVERT: R   33 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8205 (mt-10)
REVERT: R   41 ASN cc_start: 0.8344 (m-40) cc_final: 0.8049 (m110)
  outliers start: 30
  outliers final: 21
  residues processed: 137
  average time/residue: 0.1891
  time to fit residues: 34.8522
Evaluate side-chains
  135 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain R residue  114 THR
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  203 MET
Chi-restraints excluded: chain R residue  204 CYS
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  243 VAL
Chi-restraints excluded: chain R residue  250 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 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 = 0.4041 r_free = 0.4041 target = 0.162660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.126927 restraints weight = 9305.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.70
r_work: 0.3443 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7291  Z= 0.171
  Angle     :  0.554   7.667   9917  Z= 0.288
  Chirality :  0.044   0.212   1139
  Planarity :  0.004   0.038   1265
  Dihedral  :  4.494  55.062   1008
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 19.67 %
    Favored  : 76.66 %
  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:  0.49 (0.29), residues: 910
  helix:  2.03 (0.26), residues: 410
  sheet: -1.85 (0.36), residues: 172
  loop : -0.54 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 263 
 HIS   0.003   0.001   HIS R 131 
 PHE   0.014   0.001   PHE R 285 
 TYR   0.023   0.001   TYR R 187 
 ARG   0.007   0.000   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04178 (  390)
  hydrogen bonds       : angle       4.45083 ( 1131)
  SS BOND              : bond        0.00428 (    2)
  SS BOND              : angle       0.48371 (    4)
  covalent geometry    : bond        0.00399 ( 7289)
  covalent geometry    : angle       0.55417 ( 9913)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8643 (mmm-85) cc_final: 0.8432 (mtp85)
REVERT: A  220 HIS cc_start: 0.7837 (t-170) cc_final: 0.6851 (t-170)
REVERT: B  198 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8477 (pp)
REVERT: B  262 MET cc_start: 0.8154 (tpp) cc_final: 0.7766 (mmt)
REVERT: B  292 PHE cc_start: 0.8681 (m-80) cc_final: 0.8363 (m-80)
REVERT: B  329 THR cc_start: 0.9112 (m) cc_final: 0.8669 (p)
REVERT: R   33 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8246 (mt-10)
REVERT: R   41 ASN cc_start: 0.8392 (m-40) cc_final: 0.8050 (m110)
  outliers start: 27
  outliers final: 21
  residues processed: 130
  average time/residue: 0.1806
  time to fit residues: 31.8751
Evaluate side-chains
  131 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain R residue  114 THR
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  203 MET
Chi-restraints excluded: chain R residue  204 CYS
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  243 VAL
Chi-restraints excluded: chain R residue  250 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 66 optimal weight:    0.0870
   chunk 17 optimal weight:    0.1980
   chunk 46 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0000
   chunk 28 optimal weight:    1.9990
   chunk 43 optimal weight:    0.4980
   chunk 41 optimal weight:    0.2980
   chunk 55 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.2162

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
** A 375 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 = 0.4090 r_free = 0.4090 target = 0.167012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.130733 restraints weight = 9299.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 2.51
r_work: 0.3526 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.061   7291  Z= 0.113
  Angle     :  0.542  10.797   9917  Z= 0.278
  Chirality :  0.043   0.241   1139
  Planarity :  0.004   0.037   1265
  Dihedral  :  4.309  55.811   1008
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 19.95 %
    Favored  : 77.20 %
  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:  0.55 (0.29), residues: 910
  helix:  2.11 (0.26), residues: 410
  sheet: -1.80 (0.37), residues: 169
  loop : -0.59 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.002   0.000   HIS B  54 
 PHE   0.016   0.001   PHE A 222 
 TYR   0.017   0.001   TYR R 187 
 ARG   0.006   0.000   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03884 (  390)
  hydrogen bonds       : angle       4.42098 ( 1131)
  SS BOND              : bond        0.00143 (    2)
  SS BOND              : angle       0.74925 (    4)
  covalent geometry    : bond        0.00246 ( 7289)
  covalent geometry    : angle       0.54192 ( 9913)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 ASP cc_start: 0.6973 (m-30) cc_final: 0.6641 (t0)
REVERT: B  262 MET cc_start: 0.8026 (tpp) cc_final: 0.7656 (mmt)
REVERT: B  292 PHE cc_start: 0.8497 (m-80) cc_final: 0.8238 (m-80)
REVERT: B  329 THR cc_start: 0.9048 (m) cc_final: 0.8679 (p)
REVERT: B  339 TRP cc_start: 0.8783 (m100) cc_final: 0.8392 (m100)
REVERT: G   21 MET cc_start: 0.7652 (ptm) cc_final: 0.7298 (ppp)
REVERT: R   33 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8203 (mt-10)
REVERT: R   41 ASN cc_start: 0.8214 (m-40) cc_final: 0.7938 (m110)
  outliers start: 21
  outliers final: 13
  residues processed: 143
  average time/residue: 0.1972
  time to fit residues: 37.9314
Evaluate side-chains
  134 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLN
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  114 THR
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  243 VAL
Chi-restraints excluded: chain R residue  250 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0670
   chunk 34 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 88 optimal weight:    0.5980
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 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 = 0.4068 r_free = 0.4068 target = 0.164899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.128906 restraints weight = 9422.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 2.67
r_work: 0.3475 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7291  Z= 0.146
  Angle     :  0.581   9.838   9917  Z= 0.294
  Chirality :  0.044   0.257   1139
  Planarity :  0.004   0.037   1265
  Dihedral  :  4.361  55.272   1008
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 20.62 %
    Favored  : 76.80 %
  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:  0.51 (0.29), residues: 910
  helix:  2.06 (0.26), residues: 410
  sheet: -1.88 (0.36), residues: 175
  loop : -0.52 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 263 
 HIS   0.003   0.001   HIS R 131 
 PHE   0.014   0.001   PHE R 115 
 TYR   0.017   0.001   TYR R 187 
 ARG   0.006   0.000   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04050 (  390)
  hydrogen bonds       : angle       4.44448 ( 1131)
  SS BOND              : bond        0.00289 (    2)
  SS BOND              : angle       0.43382 (    4)
  covalent geometry    : bond        0.00345 ( 7289)
  covalent geometry    : angle       0.58125 ( 9913)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  246 ASP cc_start: 0.8152 (m-30) cc_final: 0.7844 (m-30)
REVERT: B  262 MET cc_start: 0.8107 (tpp) cc_final: 0.7727 (mmt)
REVERT: B  292 PHE cc_start: 0.8583 (m-80) cc_final: 0.8282 (m-80)
REVERT: B  329 THR cc_start: 0.9080 (m) cc_final: 0.8712 (p)
REVERT: G   21 MET cc_start: 0.7634 (ptm) cc_final: 0.7283 (ppp)
REVERT: R   33 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8244 (mt-10)
REVERT: R   41 ASN cc_start: 0.8255 (m-40) cc_final: 0.7964 (m110)
  outliers start: 19
  outliers final: 15
  residues processed: 128
  average time/residue: 0.1950
  time to fit residues: 33.4539
Evaluate side-chains
  126 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  114 THR
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  204 CYS
Chi-restraints excluded: chain R residue  236 MET
Chi-restraints excluded: chain R residue  243 VAL
Chi-restraints excluded: chain R residue  250 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 16 optimal weight:    0.4980
   chunk 70 optimal weight:    0.3980
   chunk 71 optimal weight:    0.9980
   chunk 79 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 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 = 0.4066 r_free = 0.4066 target = 0.164616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.129066 restraints weight = 9531.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 2.63
r_work: 0.3481 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7291  Z= 0.143
  Angle     :  0.560   7.896   9917  Z= 0.288
  Chirality :  0.044   0.242   1139
  Planarity :  0.004   0.037   1265
  Dihedral  :  4.387  55.017   1008
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 20.62 %
    Favored  : 77.07 %
  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:  0.49 (0.29), residues: 910
  helix:  2.07 (0.26), residues: 410
  sheet: -1.89 (0.35), residues: 175
  loop : -0.55 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 263 
 HIS   0.003   0.001   HIS R 131 
 PHE   0.013   0.001   PHE R 115 
 TYR   0.017   0.001   TYR R 187 
 ARG   0.006   0.000   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04046 (  390)
  hydrogen bonds       : angle       4.40710 ( 1131)
  SS BOND              : bond        0.00282 (    2)
  SS BOND              : angle       0.36327 (    4)
  covalent geometry    : bond        0.00329 ( 7289)
  covalent geometry    : angle       0.56010 ( 9913)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8669 (mmm-85) cc_final: 0.8439 (mtp85)
REVERT: A  220 HIS cc_start: 0.7761 (t-170) cc_final: 0.6838 (t-170)
REVERT: B  246 ASP cc_start: 0.8156 (m-30) cc_final: 0.7875 (m-30)
REVERT: B  262 MET cc_start: 0.8091 (tpp) cc_final: 0.7721 (mmt)
REVERT: B  292 PHE cc_start: 0.8583 (m-80) cc_final: 0.8290 (m-80)
REVERT: B  329 THR cc_start: 0.9084 (m) cc_final: 0.8706 (p)
REVERT: G   21 MET cc_start: 0.7660 (ptm) cc_final: 0.7299 (ppp)
REVERT: R   22 GLU cc_start: 0.7481 (tt0) cc_final: 0.6928 (tp30)
REVERT: R   33 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8238 (mt-10)
REVERT: R   41 ASN cc_start: 0.8253 (m-40) cc_final: 0.7964 (m110)
  outliers start: 17
  outliers final: 14
  residues processed: 128
  average time/residue: 0.1852
  time to fit residues: 32.0884
Evaluate side-chains
  128 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  114 THR
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  204 CYS
Chi-restraints excluded: chain R residue  243 VAL
Chi-restraints excluded: chain R residue  250 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 87 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0170
   chunk 65 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 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 = 0.4068 r_free = 0.4068 target = 0.165013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.128442 restraints weight = 9303.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 2.51
r_work: 0.3494 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7291  Z= 0.136
  Angle     :  0.572   8.390   9917  Z= 0.290
  Chirality :  0.043   0.234   1139
  Planarity :  0.004   0.038   1265
  Dihedral  :  4.372  55.002   1008
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.49 %
    Favored  : 77.07 %
  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:  0.47 (0.29), residues: 910
  helix:  1.98 (0.26), residues: 416
  sheet: -1.87 (0.36), residues: 175
  loop : -0.51 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 263 
 HIS   0.003   0.001   HIS R 131 
 PHE   0.012   0.001   PHE R 115 
 TYR   0.017   0.001   TYR R 187 
 ARG   0.006   0.000   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04020 (  390)
  hydrogen bonds       : angle       4.37706 ( 1131)
  SS BOND              : bond        0.00252 (    2)
  SS BOND              : angle       0.33192 (    4)
  covalent geometry    : bond        0.00311 ( 7289)
  covalent geometry    : angle       0.57179 ( 9913)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3588.80 seconds
wall clock time: 63 minutes 4.97 seconds (3784.97 seconds total)