Starting phenix.real_space_refine
on Tue Mar 11 21:51:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f8v_31493/03_2025/7f8v_31493.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f8v_31493/03_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_31493/03_2025/7f8v_31493.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f8v_31493/03_2025/7f8v_31493.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f8v_31493/03_2025/7f8v_31493.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f8v_31493/03_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-5624/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: 4.27, per 1000 atoms: 0.65
  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: 1.52
  Conformation dependent library (CDL) restraints added in 878.1 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: 0.66
  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: 1.69

  Time building geometry restraints manager: 1.77 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:             1.260
  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:                     17.970
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.560
-------------------------------------------------------------------------------
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  : 0.721 
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: 0.1777
  time to fit residues: 29.4004
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  : 0.712 
-------------------------------------------------------------------------------
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  : 0.665 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.7142 (mmm) cc_final: 0.6905 (mmm)
REVERT: A  276 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6793 (pm20)
REVERT: B  291 ASP cc_start: 0.5714 (t0) cc_final: 0.5336 (t0)
  outliers start: 10
  outliers final: 9
  residues processed: 112
  average time/residue: 0.1622
  time to fit residues: 25.0220
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  : 0.631 
-------------------------------------------------------------------------------
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:    0.9980
   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:    0.9782

-------------------------------------------------------------------------------
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 = 0.4415 r_free = 0.4415 target = 0.186841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.161148 restraints weight = 7385.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.4206 rms_B_bonded: 2.00
r_work: 0.4009 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6636
moved from start:          0.1777

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= 0.253
  Angle     :  0.602   8.244   9150  Z= 0.317
  Chirality :  0.044   0.148   1057
  Planarity :  0.005   0.045   1147
  Dihedral  :  4.885  27.803    915
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 10.67 %
    Favored  : 86.52 %
  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: -0.94 (0.28), residues: 832
  helix:  0.76 (0.28), residues: 331
  sheet: -1.17 (0.40), residues: 143
  loop : -1.70 (0.30), residues: 358

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   0.017   0.002   TYR R 238 
 ARG   0.003   0.001   ARG R 396 

*********************** 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
  117 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7580 (m-10)
REVERT: A  248 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.5616 (mtp)
REVERT: A  276 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6947 (pm20)
REVERT: B  291 ASP cc_start: 0.6004 (t0) cc_final: 0.5647 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 105
  average time/residue: 0.1573
  time to fit residues: 23.2230
Evaluate side-chains
  105 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0170
   chunk 38 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0670
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.3956

-------------------------------------------------------------------------------
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 = 0.4449 r_free = 0.4449 target = 0.190464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.165158 restraints weight = 7457.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.4244 rms_B_bonded: 1.86
r_work: 0.4069 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6541
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6743  Z= 0.167
  Angle     :  0.548   7.419   9150  Z= 0.286
  Chirality :  0.042   0.149   1057
  Planarity :  0.004   0.043   1147
  Dihedral  :  4.598  25.499    915
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 12.92 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.28), residues: 832
  helix:  1.12 (0.29), residues: 331
  sheet: -1.16 (0.40), residues: 142
  loop : -1.49 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 165 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.013   0.001   PHE R 110 
 TYR   0.011   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
  125 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7289 (m-10)
REVERT: A  276 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6874 (pm20)
REVERT: B   61 MET cc_start: 0.6902 (ppp) cc_final: 0.6443 (ppp)
REVERT: B  270 ILE cc_start: 0.6600 (mm) cc_final: 0.6262 (mt)
  outliers start: 16
  outliers final: 9
  residues processed: 117
  average time/residue: 0.1427
  time to fit residues: 23.5161
Evaluate side-chains
  105 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 19 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 10 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4479 r_free = 0.4479 target = 0.193698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.165714 restraints weight = 7025.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.4215 rms_B_bonded: 2.05
r_work: 0.4061 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3897 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6652
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6743  Z= 0.231
  Angle     :  0.587   7.924   9150  Z= 0.303
  Chirality :  0.043   0.199   1057
  Planarity :  0.004   0.043   1147
  Dihedral  :  4.706  27.439    915
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 14.47 %
    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: -0.64 (0.29), residues: 832
  helix:  1.12 (0.29), residues: 330
  sheet: -1.23 (0.40), residues: 142
  loop : -1.53 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 211 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.016   0.002   PHE R 110 
 TYR   0.011   0.002   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
  119 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
REVERT: A  200 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7544 (m-80)
REVERT: A  248 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6029 (mtp)
REVERT: A  276 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6896 (pm20)
REVERT: B  270 ILE cc_start: 0.6385 (mm) cc_final: 0.6119 (mt)
REVERT: B  291 ASP cc_start: 0.6446 (t0) cc_final: 0.6070 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 110
  average time/residue: 0.1567
  time to fit residues: 24.3387
Evaluate side-chains
  112 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
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   58 ILE
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:    0.7980
   chunk 17 optimal weight:    0.1980
   chunk 1 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 28 optimal weight:    0.4980
   chunk 54 optimal weight:    0.5980
   chunk 57 optimal weight:    0.3980
   chunk 48 optimal weight:    6.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.4504 r_free = 0.4504 target = 0.196374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.168997 restraints weight = 6937.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.4247 rms_B_bonded: 2.02
r_work: 0.4096 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3932 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6602
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6743  Z= 0.182
  Angle     :  0.568  10.775   9150  Z= 0.290
  Chirality :  0.042   0.195   1057
  Planarity :  0.004   0.043   1147
  Dihedral  :  4.602  28.173    915
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.31 %
    Favored  : 82.02 %
  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: -0.58 (0.28), residues: 832
  helix:  1.15 (0.29), residues: 336
  sheet: -1.20 (0.40), residues: 142
  loop : -1.52 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 165 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.030   0.002   PHE B 292 
 TYR   0.009   0.001   TYR A 231 
 ARG   0.002   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
  120 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7393 (m-10)
REVERT: A  248 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6083 (mtp)
REVERT: B   61 MET cc_start: 0.6872 (ppp) cc_final: 0.6436 (ppp)
REVERT: B  270 ILE cc_start: 0.6409 (mm) cc_final: 0.6133 (mt)
  outliers start: 19
  outliers final: 15
  residues processed: 109
  average time/residue: 0.1610
  time to fit residues: 24.6530
Evaluate side-chains
  111 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
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  317 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 17 optimal weight:    0.1980
   chunk 61 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.4489 r_free = 0.4489 target = 0.194685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.166500 restraints weight = 7065.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.4222 rms_B_bonded: 2.07
r_work: 0.4070 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3904 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6639
moved from start:          0.2277

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= 0.207
  Angle     :  0.574   9.448   9150  Z= 0.294
  Chirality :  0.043   0.176   1057
  Planarity :  0.004   0.044   1147
  Dihedral  :  4.637  31.184    915
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.87 %
    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: -0.63 (0.28), residues: 832
  helix:  1.13 (0.29), residues: 336
  sheet: -1.21 (0.40), residues: 143
  loop : -1.58 (0.30), residues: 353

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   0.021   0.002   PHE B 292 
 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
  118 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7482 (m-80)
REVERT: A  248 MET cc_start: 0.6746 (OUTLIER) cc_final: 0.6008 (mtp)
REVERT: A  276 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6922 (pm20)
REVERT: B   61 MET cc_start: 0.6815 (ppp) cc_final: 0.6378 (ppp)
REVERT: B  270 ILE cc_start: 0.6442 (mm) cc_final: 0.6177 (mt)
  outliers start: 20
  outliers final: 16
  residues processed: 109
  average time/residue: 0.1671
  time to fit residues: 25.1528
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  : 0.689 
-------------------------------------------------------------------------------
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 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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 60 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0470
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0870
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.4256

-------------------------------------------------------------------------------
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 = 0.4510 r_free = 0.4510 target = 0.197018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.169335 restraints weight = 7010.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.4252 rms_B_bonded: 2.05
r_work: 0.4099 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3937 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6599
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6743  Z= 0.172
  Angle     :  0.563   9.097   9150  Z= 0.287
  Chirality :  0.042   0.157   1057
  Planarity :  0.004   0.044   1147
  Dihedral  :  4.537  31.483    915
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.57 %
    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: -0.54 (0.29), residues: 832
  helix:  1.22 (0.29), residues: 337
  sheet: -1.20 (0.40), residues: 143
  loop : -1.54 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 165 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.017   0.002   PHE A 275 
 TYR   0.008   0.001   TYR R 238 
 ARG   0.002   0.000   ARG B 219 

*********************** 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
  117 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.5985 (mtp)
REVERT: A  276 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6955 (pm20)
REVERT: B   61 MET cc_start: 0.6827 (ppp) cc_final: 0.6461 (ppp)
REVERT: B  270 ILE cc_start: 0.6393 (mm) cc_final: 0.6136 (mt)
REVERT: R  353 ASN cc_start: 0.7211 (m-40) cc_final: 0.6542 (m110)
  outliers start: 15
  outliers final: 13
  residues processed: 110
  average time/residue: 0.1681
  time to fit residues: 25.6772
Evaluate side-chains
  113 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 4 optimal weight:    0.0980
   chunk 52 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    0.3980
   chunk 31 optimal weight:    4.9990
   chunk 71 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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
A 332 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.196187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.168234 restraints weight = 7087.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.4240 rms_B_bonded: 2.08
r_work: 0.4088 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3924 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6621
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6743  Z= 0.191
  Angle     :  0.570   8.927   9150  Z= 0.291
  Chirality :  0.043   0.211   1057
  Planarity :  0.004   0.044   1147
  Dihedral  :  4.539  31.707    915
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  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: -0.52 (0.29), residues: 832
  helix:  1.24 (0.29), residues: 337
  sheet: -1.08 (0.40), residues: 149
  loop : -1.60 (0.30), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP R 346 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.017   0.002   PHE A 275 
 TYR   0.009   0.001   TYR R 238 
 ARG   0.002   0.000   ARG R 152 

*********************** 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
  117 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7426 (m-80)
REVERT: A  248 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.6023 (mtp)
REVERT: A  276 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6951 (pm20)
REVERT: A  332 ASN cc_start: 0.5679 (OUTLIER) cc_final: 0.5437 (m-40)
REVERT: B   61 MET cc_start: 0.6871 (ppp) cc_final: 0.6443 (ppp)
REVERT: B  270 ILE cc_start: 0.6402 (mm) cc_final: 0.6145 (mt)
REVERT: R  353 ASN cc_start: 0.7222 (m-40) cc_final: 0.6845 (m-40)
  outliers start: 18
  outliers final: 13
  residues processed: 110
  average time/residue: 0.1655
  time to fit residues: 25.0716
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  : 0.661 
-------------------------------------------------------------------------------
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  332 ASN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0970
   chunk 41 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 4 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.4499 r_free = 0.4499 target = 0.195708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.167303 restraints weight = 7108.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.4229 rms_B_bonded: 2.12
r_work: 0.4081 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3914 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6630
moved from start:          0.2448

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= 0.200
  Angle     :  0.589   8.806   9150  Z= 0.303
  Chirality :  0.043   0.259   1057
  Planarity :  0.004   0.044   1147
  Dihedral  :  4.593  32.047    915
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 16.85 %
    Favored  : 80.48 %
  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:  1.16 (0.29), residues: 336
  sheet: -1.12 (0.40), residues: 148
  loop : -1.61 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 165 
 HIS   0.008   0.001   HIS B 225 
 PHE   0.019   0.002   PHE A 337 
 TYR   0.010   0.001   TYR R 380 
 ARG   0.003   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: 19
    poor density    : 97
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6088 (mtp)
REVERT: A  276 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6954 (pm20)
REVERT: A  332 ASN cc_start: 0.5681 (OUTLIER) cc_final: 0.5316 (m-40)
REVERT: B  270 ILE cc_start: 0.6386 (mm) cc_final: 0.6156 (mt)
REVERT: R  353 ASN cc_start: 0.7249 (m-40) cc_final: 0.6760 (m-40)
  outliers start: 19
  outliers final: 14
  residues processed: 108
  average time/residue: 0.1690
  time to fit residues: 25.8039
Evaluate side-chains
  110 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
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  332 ASN
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  234 PHE
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  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:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   chunk 75 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0570
   chunk 0 optimal weight:   10.0000
   chunk 80 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.4500 r_free = 0.4500 target = 0.195923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.167747 restraints weight = 7138.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.4233 rms_B_bonded: 2.10
r_work: 0.4081 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3914 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6630
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.103   6743  Z= 0.236
  Angle     :  0.983  59.177   9150  Z= 0.580
  Chirality :  0.044   0.262   1057
  Planarity :  0.004   0.044   1147
  Dihedral  :  4.629  32.052    915
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 16.99 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.13 %
  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: -0.61 (0.28), residues: 832
  helix:  1.15 (0.29), residues: 336
  sheet: -1.12 (0.40), residues: 148
  loop : -1.61 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP R 165 
 HIS   0.007   0.001   HIS B 225 
 PHE   0.021   0.002   PHE A 200 
 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: 4215.61 seconds
wall clock time: 72 minutes 54.75 seconds (4374.75 seconds total)