Starting phenix.real_space_refine
on Tue Feb 11 22:21:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f8v_31493/02_2025/7f8v_31493.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f8v_31493/02_2025/7f8v_31493.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f8v_31493/02_2025/7f8v_31493.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f8v_31493/02_2025/7f8v_31493.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f8v_31493/02_2025/7f8v_31493.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f8v_31493/02_2025/7f8v_31493.cif"
  }
  resolution = 3.3
  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=   0.003
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      53      5.16       5
     C    4224      2.51       5
     N    1127      2.21       5
     O    1197      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6601
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1748
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2347
          Classifications: {'peptide': 306}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 300}
    Chain: "C"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 245
          Classifications: {'peptide': 33}
          Link IDs: {'PTRANS': 4, 'TRANS': 28}
    Chain: "E"
      Number of atoms: 133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 133
          Classifications: {'peptide': 17}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 15}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'PCA:plan-2': 1, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 17
    Chain: "R"
      Number of atoms: 2128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2128
          Classifications: {'peptide': 275}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 13, 'TRANS': 261}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ALA A 236 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA A 236 " occ=0.00
  Time building chain proxies: 4.21, per 1000 atoms: 0.64
  Number of scatterers: 6601
  At special positions: 0
  Unit cell: (110.77, 117.04, 81.51, 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      53     16.00
     O    1197      8.00
     N    1127      7.00
     C    4224      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 127 " - pdb=" SG  CYS R 205 " distance=2.04

  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: 1.61
  Conformation dependent library (CDL) restraints added in 985.2 milliseconds
  

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1592

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 11 sheets defined
      43.5% alpha, 16.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 29
    Processing helix  chain 'A' and resid 45 through 52
      removed outlier: 3.607A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
      removed outlier: 3.517A  pdb=" N   LYS A 211 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TRP A 212 " --> pdb=" O   ARG A 209 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   ILE A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 232
      removed outlier: 4.254A  pdb=" N   ASP A 232 " --> pdb=" O   SER A 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 229 through 232'
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 257 through 261
      removed outlier: 3.583A  pdb=" N   PHE A 260 " --> pdb=" O   ASN A 257 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   THR A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 257 through 261'
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 5.208A  pdb=" N   GLU A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 331 through 352
    Processing helix  chain 'C' and resid 30 through 45
    Processing helix  chain 'R' and resid 56 through 81
      removed outlier: 4.475A  pdb=" N   ASN R  72 " --> pdb=" O   SER R  68 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU R  81 " --> pdb=" O   VAL R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 107
    Processing helix  chain 'R' and resid 107 through 117
      removed outlier: 3.612A  pdb=" N   LEU R 113 " --> pdb=" O   PRO R 109 " (cutoff:3.500A)
      Proline residue:  R 114  - end of helix
    Processing helix  chain 'R' and resid 123 through 157
    Processing helix  chain 'R' and resid 158 through 166
      removed outlier: 3.558A  pdb=" N   ALA R 162 " --> pdb=" O   ARG R 158 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 167 through 186
    Processing helix  chain 'R' and resid 187 through 192
    Processing helix  chain 'R' and resid 211 through 227
    Processing helix  chain 'R' and resid 227 through 248
    Processing helix  chain 'R' and resid 327 through 360
      removed outlier: 4.132A  pdb=" N   ARG R 333 " --> pdb=" O   LYS R 329 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   MET R 334 " --> pdb=" O   ARG R 330 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   VAL R 339 " --> pdb=" O   LEU R 335 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   PHE R 342 " --> pdb=" O   ILE R 338 " (cutoff:3.500A)
      Proline residue:  R 348  - end of helix
    Processing helix  chain 'R' and resid 362 through 367
      removed outlier: 3.725A  pdb=" N   ALA R 366 " --> pdb=" O   GLY R 362 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU R 367 " --> pdb=" O   ALA R 363 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 362 through 367'
    Processing helix  chain 'R' and resid 369 through 391
      removed outlier: 4.091A  pdb=" N   LEU R 377 " --> pdb=" O   SER R 373 " (cutoff:3.500A)
      Proline residue:  R 387  - end of helix
      removed outlier: 3.678A  pdb=" N   TYR R 390 " --> pdb=" O   ASN R 386 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   CYS R 391 " --> pdb=" O   PRO R 387 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 394 through 405
      removed outlier: 3.837A  pdb=" N   ARG R 398 " --> pdb=" O   HIS R 394 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 192
    Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 227
      removed outlier: 5.613A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   ILE A 265 " --> pdb=" O   TYR A 321 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   HIS A 323 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   LEU A 267 " --> pdb=" O   HIS A 323 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.517A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.894A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105
      removed outlier: 5.898A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.135A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.098A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.405A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.995A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 276
    Processing sheet with id=AB1, first strand: chain 'B' and resid 295 through 296
      removed outlier: 3.677A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 197 through 198
      removed outlier: 3.699A  pdb=" N   VAL R 202 " --> pdb=" O   VAL R 198 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    942 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: 1.82

  Time building geometry restraints manager: 1.84 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1238
        1.33 -     1.45: 1708
        1.45 -     1.57: 3720
        1.57 -     1.70: 0
        1.70 -     1.82: 77
  Bond restraints: 6743
  Sorted by residual:
  bond pdb=" N   LEU A 284 "
       pdb=" CA  LEU A 284 "
    ideal  model  delta    sigma   weight residual
    1.458  1.500 -0.041 1.37e-02 5.33e+03 9.10e+00
  bond pdb=" C   ALA R 370 "
       pdb=" N   PRO R 371 "
    ideal  model  delta    sigma   weight residual
    1.334  1.399 -0.065 2.34e-02 1.83e+03 7.66e+00
  bond pdb=" N   MET R 134 "
       pdb=" CA  MET R 134 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.17e-02 7.31e+03 6.42e+00
  bond pdb=" CA  ASP B 291 "
       pdb=" C   ASP B 291 "
    ideal  model  delta    sigma   weight residual
    1.523  1.548 -0.025 1.34e-02 5.57e+03 3.48e+00
  bond pdb=" C   TYR R 189 "
       pdb=" N   PRO R 190 "
    ideal  model  delta    sigma   weight residual
    1.336  1.352 -0.016 9.80e-03 1.04e+04 2.83e+00
  ... (remaining 6738 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 8787
        1.98 -     3.96: 291
        3.96 -     5.95: 57
        5.95 -     7.93: 9
        7.93 -     9.91: 6
  Bond angle restraints: 9150
  Sorted by residual:
  angle pdb=" N   PCA E   1 "
        pdb=" CA  PCA E   1 "
        pdb=" CB  PCA E   1 "
      ideal   model   delta    sigma   weight residual
     110.50  102.21    8.29 1.70e+00 3.46e-01 2.38e+01
  angle pdb=" N   PRO E   3 "
        pdb=" CA  PRO E   3 "
        pdb=" C   PRO E   3 "
      ideal   model   delta    sigma   weight residual
     112.47  104.67    7.80 2.06e+00 2.36e-01 1.43e+01
  angle pdb=" CB  MET A  18 "
        pdb=" CG  MET A  18 "
        pdb=" SD  MET A  18 "
      ideal   model   delta    sigma   weight residual
     112.70  122.52   -9.82 3.00e+00 1.11e-01 1.07e+01
  angle pdb=" C   MET R 134 "
        pdb=" CA  MET R 134 "
        pdb=" CB  MET R 134 "
      ideal   model   delta    sigma   weight residual
     110.96  106.03    4.93 1.54e+00 4.22e-01 1.02e+01
  angle pdb=" CA  MET R 108 "
        pdb=" CB  MET R 108 "
        pdb=" CG  MET R 108 "
      ideal   model   delta    sigma   weight residual
     114.10  120.15   -6.05 2.00e+00 2.50e-01 9.14e+00
  ... (remaining 9145 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 3600
       17.86 -    35.72: 308
       35.72 -    53.58: 61
       53.58 -    71.44: 9
       71.44 -    89.30: 6
  Dihedral angle restraints: 3984
    sinusoidal: 1526
      harmonic: 2458
  Sorted by residual:
  dihedral pdb=" CB  CYS R 127 "
           pdb=" SG  CYS R 127 "
           pdb=" SG  CYS R 205 "
           pdb=" CB  CYS R 205 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  175.61  -82.61     1      1.00e+01 1.00e-02 8.37e+01
  dihedral pdb=" CA  CYS R 107 "
           pdb=" C   CYS R 107 "
           pdb=" N   MET R 108 "
           pdb=" CA  MET R 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.49  -20.51     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  MET R 186 "
           pdb=" C   MET R 186 "
           pdb=" N   VAL R 187 "
           pdb=" CA  VAL R 187 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.39   19.61     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 3981 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 779
       0.054 -    0.108: 218
       0.108 -    0.161: 52
       0.161 -    0.215: 4
       0.215 -    0.269: 4
  Chirality restraints: 1057
  Sorted by residual:
  chirality pdb=" CA  MET R 108 "
            pdb=" N   MET R 108 "
            pdb=" C   MET R 108 "
            pdb=" CB  MET R 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  MET R 134 "
            pdb=" N   MET R 134 "
            pdb=" C   MET R 134 "
            pdb=" CB  MET R 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CB  THR R 178 "
            pdb=" CA  THR R 178 "
            pdb=" OG1 THR R 178 "
            pdb=" CG2 THR R 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1054 not shown)

  Planarity restraints: 1147
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   PCA E   1 "   -0.136 2.00e-02 2.50e+03   9.12e-02 1.04e+02
        pdb=" CA  PCA E   1 "    0.115 2.00e-02 2.50e+03
        pdb=" CG  PCA E   1 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD  PCA E   1 "   -0.024 2.00e-02 2.50e+03
        pdb=" OE  PCA E   1 "    0.087 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 288 "    0.044 5.00e-02 4.00e+02   6.70e-02 7.18e+00
        pdb=" N   PRO A 289 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 289 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 289 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  52 "    0.044 5.00e-02 4.00e+02   6.63e-02 7.03e+00
        pdb=" N   PRO C  53 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO C  53 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C  53 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1144 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1360
        2.78 -     3.31: 6306
        3.31 -     3.84: 11190
        3.84 -     4.37: 13216
        4.37 -     4.90: 22806
  Nonbonded interactions: 54878
  Sorted by model distance:
  nonbonded pdb=" O   HIS R 364 "
            pdb=" OG  SER R 368 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG1 THR B  65 "
            pdb=" O   PRO B 107 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OE1 GLN B 176 "
            pdb=" OG1 THR B 179 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   MET B 325 "
            pdb=" ND2 ASN B 340 "
     model   vdw
     2.310 3.120
  ... (remaining 54873 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.730
  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:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.450
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6272
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      :  0.005   0.068   6743  Z= 0.321
  Angle     :  0.873   9.912   9150  Z= 0.467
  Chirality :  0.054   0.269   1057
  Planarity :  0.007   0.091   1147
  Dihedral  : 14.097  89.299   2389
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.26), residues: 832
  helix: -0.08 (0.27), residues: 331
  sheet: -1.03 (0.41), residues: 131
  loop : -1.78 (0.28), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP B 211 
 HIS   0.013   0.002   HIS A 281 
 PHE   0.026   0.002   PHE R 343 
 TYR   0.016   0.003   TYR A 231 
 ARG   0.010   0.001   ARG R 398 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
REVERT: B  118 ASP cc_start: 0.7171 (t0) cc_final: 0.6889 (t0)
REVERT: C   32 LYS cc_start: 0.7713 (mppt) cc_final: 0.7474 (mtmm)
REVERT: E    5 LEU cc_start: 0.5831 (pt) cc_final: 0.5492 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1859
  time to fit residues: 30.6554
Evaluate side-chains
  100 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 34 optimal weight:    0.4980
   chunk 21 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   chunk 74 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:
R 204 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.190563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.164954 restraints weight = 7264.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.4242 rms_B_bonded: 1.98
r_work: 0.4051 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6567
moved from start:          0.1333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6743  Z= 0.231
  Angle     :  0.616   8.898   9150  Z= 0.322
  Chirality :  0.044   0.175   1057
  Planarity :  0.005   0.050   1147
  Dihedral  :  4.875  18.280    915
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  8.01 %
    Favored  : 90.59 %
  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: -0.93 (0.27), residues: 832
  helix:  0.66 (0.28), residues: 332
  sheet: -0.94 (0.40), residues: 143
  loop : -1.69 (0.29), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  99 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.015   0.002   PHE B 234 
 TYR   0.014   0.002   TYR A 231 
 ARG   0.007   0.000   ARG R 152 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.7143 (mmm) cc_final: 0.6907 (mmm)
REVERT: A  276 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6794 (pm20)
REVERT: B  291 ASP cc_start: 0.5713 (t0) cc_final: 0.5333 (t0)
  outliers start: 10
  outliers final: 9
  residues processed: 112
  average time/residue: 0.1660
  time to fit residues: 25.6225
Evaluate side-chains
  106 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   chunk 44 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 68 optimal weight:    0.3980
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
R 166 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.184755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.158313 restraints weight = 7425.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.4178 rms_B_bonded: 2.05
r_work: 0.3987 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6672
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6743  Z= 0.290
  Angle     :  0.630   8.343   9150  Z= 0.332
  Chirality :  0.045   0.160   1057
  Planarity :  0.005   0.046   1147
  Dihedral  :  5.014  30.019    915
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 11.24 %
    Favored  : 85.96 %
  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: -1.08 (0.28), residues: 832
  helix:  0.62 (0.28), residues: 331
  sheet: -1.24 (0.40), residues: 143
  loop : -1.76 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  99 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.017   0.002   PHE B 234 
 TYR   0.018   0.002   TYR R 238 
 ARG   0.003   0.001   ARG R  57 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7706 (m-10)
REVERT: A  248 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.5697 (mtp)
REVERT: A  276 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6960 (pm20)
REVERT: B  325 MET cc_start: 0.6198 (tpt) cc_final: 0.5971 (tpt)
  outliers start: 20
  outliers final: 14
  residues processed: 109
  average time/residue: 0.1677
  time to fit residues: 25.2156
Evaluate side-chains
  107 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  108 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 6 optimal weight:    0.4980
   chunk 39 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0670
   chunk 38 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0670
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.4456

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS
A 332 ASN
R 166 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.196414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.167123 restraints weight = 7107.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.4222 rms_B_bonded: 2.22
r_work: 0.4083 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6465
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6743  Z= 0.180
  Angle     :  0.554   7.605   9150  Z= 0.290
  Chirality :  0.042   0.174   1057
  Planarity :  0.004   0.044   1147
  Dihedral  :  4.692  26.708    915
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.62 %
    Favored  : 83.99 %
  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: -0.70 (0.28), residues: 832
  helix:  1.01 (0.28), residues: 330
  sheet: -1.22 (0.40), residues: 142
  loop : -1.53 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 165 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.016   0.001   PHE R 110 
 TYR   0.012   0.001   TYR R 238 
 ARG   0.002   0.000   ARG R 356 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.728 
Fit side-chains
   revert: symmetry clash
REVERT: A  200 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7227 (m-10)
REVERT: A  248 MET cc_start: 0.6687 (OUTLIER) cc_final: 0.5851 (mtp)
REVERT: A  276 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6904 (pm20)
REVERT: B  270 ILE cc_start: 0.6629 (mm) cc_final: 0.6265 (mt)
  outliers start: 17
  outliers final: 10
  residues processed: 111
  average time/residue: 0.1731
  time to fit residues: 26.2317
Evaluate side-chains
  109 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 49 optimal weight:    0.3980
   chunk 19 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS
A 332 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.194366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.165670 restraints weight = 6998.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.4212 rms_B_bonded: 2.14
r_work: 0.4060 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6499
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6743  Z= 0.216
  Angle     :  0.573   7.877   9150  Z= 0.297
  Chirality :  0.042   0.175   1057
  Planarity :  0.004   0.044   1147
  Dihedral  :  4.688  27.313    915
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 14.61 %
    Favored  : 82.87 %
  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: -0.65 (0.29), residues: 832
  helix:  1.10 (0.29), residues: 330
  sheet: -1.23 (0.40), residues: 142
  loop : -1.54 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 211 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.029   0.002   PHE B 292 
 TYR   0.010   0.001   TYR R 238 
 ARG   0.003   0.000   ARG R 152 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7358 (m-10)
REVERT: A  248 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.5858 (mtp)
REVERT: A  276 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6867 (pm20)
REVERT: B   61 MET cc_start: 0.6713 (ppp) cc_final: 0.6249 (ppp)
REVERT: B  270 ILE cc_start: 0.6396 (mm) cc_final: 0.6115 (mt)
  outliers start: 18
  outliers final: 14
  residues processed: 113
  average time/residue: 0.1659
  time to fit residues: 25.9896
Evaluate side-chains
  112 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  331 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 45 optimal weight:    0.4980
   chunk 27 optimal weight:    0.0470
   chunk 19 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0570
   chunk 57 optimal weight:    0.4980
   chunk 48 optimal weight:    7.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS
A 332 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.197347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.169952 restraints weight = 6934.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.4258 rms_B_bonded: 2.03
r_work: 0.4102 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3938 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6591
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6743  Z= 0.170
  Angle     :  0.554  10.931   9150  Z= 0.285
  Chirality :  0.042   0.129   1057
  Planarity :  0.004   0.044   1147
  Dihedral  :  4.561  29.349    915
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 16.43 %
    Favored  : 81.32 %
  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: -0.52 (0.29), residues: 832
  helix:  1.22 (0.29), residues: 330
  sheet: -1.19 (0.40), residues: 142
  loop : -1.48 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP R 165 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.023   0.002   PHE A 275 
 TYR   0.009   0.001   TYR A 231 
 ARG   0.003   0.000   ARG A 243 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 MET cc_start: 0.6840 (ppp) cc_final: 0.6444 (ppp)
REVERT: B  270 ILE cc_start: 0.6318 (mm) cc_final: 0.6046 (mt)
  outliers start: 16
  outliers final: 13
  residues processed: 109
  average time/residue: 0.1740
  time to fit residues: 26.1408
Evaluate side-chains
  111 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  331 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 60 optimal weight:    0.0470
   chunk 52 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.195091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.166312 restraints weight = 7053.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.4217 rms_B_bonded: 2.16
r_work: 0.4078 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3903 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6640
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6743  Z= 0.212
  Angle     :  0.565   9.983   9150  Z= 0.293
  Chirality :  0.043   0.177   1057
  Planarity :  0.004   0.044   1147
  Dihedral  :  4.608  29.685    915
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 16.01 %
    Favored  : 81.18 %
  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: -0.59 (0.28), residues: 832
  helix:  1.19 (0.29), residues: 330
  sheet: -1.21 (0.40), residues: 143
  loop : -1.54 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 211 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.018   0.002   PHE A 275 
 TYR   0.010   0.001   TYR R 238 
 ARG   0.003   0.000   ARG R 152 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6042 (mtp)
REVERT: A  276 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6971 (pm20)
REVERT: B  270 ILE cc_start: 0.6341 (mm) cc_final: 0.6075 (mt)
REVERT: R  134 MET cc_start: 0.5452 (mmp) cc_final: 0.4728 (mmt)
  outliers start: 20
  outliers final: 16
  residues processed: 110
  average time/residue: 0.1782
  time to fit residues: 27.1483
Evaluate side-chains
  115 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  331 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 78 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 6 optimal weight:    0.4980
   chunk 43 optimal weight:    3.9990
   chunk 70 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 196 HIS
A 332 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.195032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.166987 restraints weight = 7020.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.4227 rms_B_bonded: 2.06
r_work: 0.4074 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3907 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6639
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6743  Z= 0.205
  Angle     :  0.563   9.560   9150  Z= 0.291
  Chirality :  0.042   0.133   1057
  Planarity :  0.004   0.044   1147
  Dihedral  :  4.627  28.747    915
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 16.57 %
    Favored  : 80.62 %
  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: -0.63 (0.28), residues: 832
  helix:  1.16 (0.29), residues: 330
  sheet: -1.22 (0.41), residues: 142
  loop : -1.57 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 165 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.016   0.002   PHE A 275 
 TYR   0.010   0.001   TYR R 238 
 ARG   0.003   0.000   ARG R 152 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.5899 (mtp)
REVERT: A  276 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6955 (pm20)
REVERT: B   61 MET cc_start: 0.6792 (ppp) cc_final: 0.6485 (ppp)
REVERT: B  270 ILE cc_start: 0.6407 (mm) cc_final: 0.6140 (mt)
REVERT: R  134 MET cc_start: 0.5524 (mmp) cc_final: 0.4835 (mmt)
REVERT: R  353 ASN cc_start: 0.7322 (m-40) cc_final: 0.6901 (m110)
  outliers start: 20
  outliers final: 17
  residues processed: 109
  average time/residue: 0.1734
  time to fit residues: 25.9521
Evaluate side-chains
  113 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   44 HIS
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  108 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  331 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0000
   chunk 50 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 12 optimal weight:    0.3980
   chunk 31 optimal weight:    0.0030
   chunk 71 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   overall best weight:    0.3594

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 196 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.197777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.170074 restraints weight = 7052.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.4258 rms_B_bonded: 2.06
r_work: 0.4105 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3939 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6591
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6743  Z= 0.165
  Angle     :  0.546   9.267   9150  Z= 0.282
  Chirality :  0.042   0.128   1057
  Planarity :  0.004   0.044   1147
  Dihedral  :  4.498  29.016    915
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.71 %
    Favored  : 80.76 %
  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: -0.54 (0.28), residues: 832
  helix:  1.21 (0.29), residues: 337
  sheet: -1.09 (0.40), residues: 149
  loop : -1.59 (0.30), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP R 346 
 HIS   0.007   0.001   HIS B 225 
 PHE   0.021   0.001   PHE A 337 
 TYR   0.008   0.001   TYR R 238 
 ARG   0.003   0.000   ARG B 251 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.5886 (mtp)
REVERT: A  276 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6927 (pm20)
REVERT: B   61 MET cc_start: 0.6745 (ppp) cc_final: 0.6449 (ppp)
REVERT: B  270 ILE cc_start: 0.6441 (mm) cc_final: 0.6172 (mt)
REVERT: R  134 MET cc_start: 0.5405 (mmp) cc_final: 0.4689 (mmt)
REVERT: R  353 ASN cc_start: 0.7205 (m-40) cc_final: 0.6780 (m110)
  outliers start: 18
  outliers final: 15
  residues processed: 110
  average time/residue: 0.1642
  time to fit residues: 25.1574
Evaluate side-chains
  115 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  108 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  331 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS
A 270 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.194016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.165574 restraints weight = 7134.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.4211 rms_B_bonded: 2.11
r_work: 0.4056 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3892 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6662
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6743  Z= 0.231
  Angle     :  0.588   9.113   9150  Z= 0.305
  Chirality :  0.043   0.150   1057
  Planarity :  0.004   0.044   1147
  Dihedral  :  4.660  29.157    915
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.13 %
    Favored  : 80.34 %
  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: -0.70 (0.28), residues: 832
  helix:  1.08 (0.29), residues: 336
  sheet: -1.17 (0.40), residues: 148
  loop : -1.67 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP R 165 
 HIS   0.007   0.001   HIS B 225 
 PHE   0.019   0.002   PHE B 199 
 TYR   0.011   0.002   TYR R 238 
 ARG   0.004   0.000   ARG R 152 

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.5971 (mtp)
REVERT: A  276 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6960 (pm20)
REVERT: B   61 MET cc_start: 0.6882 (ppp) cc_final: 0.6462 (ppp)
REVERT: B  270 ILE cc_start: 0.6515 (mm) cc_final: 0.6237 (mt)
REVERT: B  292 PHE cc_start: 0.7231 (m-10) cc_final: 0.6849 (m-10)
REVERT: R  134 MET cc_start: 0.5587 (mmp) cc_final: 0.4911 (mmt)
REVERT: R  353 ASN cc_start: 0.7352 (m-40) cc_final: 0.6935 (m110)
  outliers start: 18
  outliers final: 16
  residues processed: 107
  average time/residue: 0.1705
  time to fit residues: 25.0695
Evaluate side-chains
  114 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  108 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  331 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0040
   chunk 70 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 80 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS
A 270 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.195081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.166850 restraints weight = 7118.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.4225 rms_B_bonded: 2.10
r_work: 0.4071 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3904 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6639
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6743  Z= 0.199
  Angle     :  0.570   8.906   9150  Z= 0.295
  Chirality :  0.042   0.141   1057
  Planarity :  0.004   0.044   1147
  Dihedral  :  4.629  29.811    915
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 16.99 %
    Favored  : 80.34 %
  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 (0.28), residues: 832
  helix:  1.11 (0.29), residues: 335
  sheet: -1.13 (0.40), residues: 147
  loop : -1.66 (0.30), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP R 165 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.021   0.002   PHE B 199 
 TYR   0.011   0.001   TYR R 238 
 ARG   0.002   0.000   ARG R 152 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4114.79 seconds
wall clock time: 73 minutes 38.51 seconds (4418.51 seconds total)