Starting phenix.real_space_refine
on Thu Feb 13 01:05:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yjn_33875/02_2025/7yjn_33875.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yjn_33875/02_2025/7yjn_33875.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yjn_33875/02_2025/7yjn_33875.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yjn_33875/02_2025/7yjn_33875.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yjn_33875/02_2025/7yjn_33875.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yjn_33875/02_2025/7yjn_33875.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.101
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      49      5.16       5
     C    5476      2.51       5
     N    1445      2.21       5
     O    1557      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 92 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8528
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 418, 3230
          Classifications: {'peptide': 418}
          Link IDs: {'PTRANS': 17, 'TRANS': 400}
    Chain: "B"
      Number of atoms: 3592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 465, 3592
          Classifications: {'peptide': 465}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 21, 'TRANS': 443}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 40
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'TRP:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "D"
      Number of atoms: 1122
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1122
          Classifications: {'peptide': 138}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 131}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "E"
      Number of atoms: 186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 186
          Classifications: {'peptide': 27}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 2, 'TRANS': 24}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "C"
      Number of atoms: 383
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 383
          Classifications: {'peptide': 47}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'TRANS': 46}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 44
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'PLP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 5.17, per 1000 atoms: 0.61
  Number of scatterers: 8528
  At special positions: 0
  Unit cell: (89.64, 82.08, 117.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      49     16.00
     P       1     15.00
     O    1557      8.00
     N    1445      7.00
     C    5476      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.13
  Conformation dependent library (CDL) restraints added in 972.7 milliseconds
  

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2030

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 5 sheets defined
      51.5% alpha, 6.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 73
      removed outlier: 3.857A  pdb=" N   ASP A  70 " --> pdb=" O   GLU A  66 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   GLU A  71 " --> pdb=" O   GLN A  67 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A  72 " --> pdb=" O   GLU A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 140
      removed outlier: 3.546A  pdb=" N   LEU A 129 " --> pdb=" O   HIS A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 168
      removed outlier: 3.812A  pdb=" N   LEU A 157 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 190
      removed outlier: 3.615A  pdb=" N   THR A 181 " --> pdb=" O   TYR A 177 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   MET A 182 " --> pdb=" O   GLY A 178 " (cutoff:3.500A)
      Proline residue:  A 187  - end of helix
      removed outlier: 3.711A  pdb=" N   CYS A 190 " --> pdb=" O   ILE A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 213
      removed outlier: 3.552A  pdb=" N   GLY A 209 " --> pdb=" O   GLY A 205 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLN A 211 " --> pdb=" O   GLN A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 239
    Processing helix  chain 'A' and resid 263 through 275
      removed outlier: 3.697A  pdb=" N   ILE A 267 " --> pdb=" O   PRO A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 300
      removed outlier: 3.777A  pdb=" N   HIS A 299 " --> pdb=" O   GLY A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 338
    Processing helix  chain 'A' and resid 349 through 365
      removed outlier: 3.618A  pdb=" N   ALA A 353 " --> pdb=" O   PRO A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 385
    Processing helix  chain 'A' and resid 411 through 431
    Processing helix  chain 'A' and resid 460 through 480
      removed outlier: 3.714A  pdb=" N   LEU A 464 " --> pdb=" O   SER A 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 36
    Processing helix  chain 'B' and resid 54 through 63
    Processing helix  chain 'B' and resid 119 through 132
      removed outlier: 3.913A  pdb=" N   ARG B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 160
    Processing helix  chain 'B' and resid 169 through 182
      Proline residue:  B 179  - end of helix
    Processing helix  chain 'B' and resid 195 through 204
    Processing helix  chain 'B' and resid 216 through 230
    Processing helix  chain 'B' and resid 258 through 267
    Processing helix  chain 'B' and resid 290 through 295
      removed outlier: 3.792A  pdb=" N   LEU B 294 " --> pdb=" O   GLY B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 314
      removed outlier: 3.884A  pdb=" N   GLY B 314 " --> pdb=" O   THR B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 334
      removed outlier: 3.682A  pdb=" N   GLN B 328 " --> pdb=" O   LYS B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 339
    Processing helix  chain 'B' and resid 344 through 359
    Processing helix  chain 'B' and resid 369 through 389
      removed outlier: 3.596A  pdb=" N   GLY B 389 " --> pdb=" O   LEU B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 421
      removed outlier: 3.553A  pdb=" N   ALA B 413 " --> pdb=" O   ALA B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 468
    Processing helix  chain 'D' and resid 25 through 45
      removed outlier: 3.791A  pdb=" N   MET D  31 " --> pdb=" O   TRP D  27 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER D  45 " --> pdb=" O   VAL D  41 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 71
    Processing helix  chain 'D' and resid 87 through 92
    Processing helix  chain 'D' and resid 93 through 96
    Processing helix  chain 'D' and resid 99 through 119
      Proline residue:  D 109  - end of helix
    Processing helix  chain 'D' and resid 124 through 141
      removed outlier: 3.708A  pdb=" N   LYS D 141 " --> pdb=" O   LEU D 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 37 through 54
      removed outlier: 3.563A  pdb=" N   ARG E  54 " --> pdb=" O   ILE E  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 15
    Processing helix  chain 'C' and resid 21 through 47
      removed outlier: 3.845A  pdb=" N   VAL C  32 " --> pdb=" O   PHE C  28 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   VAL C  33 " --> pdb=" O   ASN C  29 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 175
      removed outlier: 6.648A  pdb=" N   VAL A 278 " --> pdb=" O   VAL A 309 " (cutoff:3.500A)
      removed outlier: 8.393A  pdb=" N   THR A 311 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   LEU A 280 " --> pdb=" O   THR A 311 " (cutoff:3.500A)
      removed outlier: 8.602A  pdb=" N   ALA A 313 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ARG A 247 " --> pdb=" O   ARG A 277 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   ILE A 279 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ILE A 249 " --> pdb=" O   ILE A 279 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   ASP A 281 " --> pdb=" O   ILE A 249 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   ALA A 251 " --> pdb=" O   ASP A 281 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   VAL A 195 " --> pdb=" O   TYR A 248 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   VAL A 250 " --> pdb=" O   VAL A 195 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 390 through 392
      removed outlier: 3.699A  pdb=" N   VAL A 435 " --> pdb=" O   LYS A 452 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 85
      removed outlier: 6.147A  pdb=" N   GLU B  83 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   THR B  96 " --> pdb=" O   GLU B  83 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   TYR B  85 " --> pdb=" O   LYS B  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 163 through 167
      removed outlier: 3.636A  pdb=" N   ALA B 163 " --> pdb=" O   GLY B 322 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLY B 318 " --> pdb=" O   PHE B 167 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   VAL B 304 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASP B 191 " --> pdb=" O   VAL B 245 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   PHE B 212 " --> pdb=" O   SER B 190 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 400 through 404
      removed outlier: 3.501A  pdb=" N   MET B 401 " --> pdb=" O   ILE B 442 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ILE B 442 " --> pdb=" O   MET B 401 " (cutoff:3.500A)

    413 hydrogen bonds defined for protein.
    1224 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.21

  Time building geometry restraints manager: 2.38 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1363
        1.27 -     1.40: 2196
        1.40 -     1.54: 5003
        1.54 -     1.67: 80
        1.67 -     1.81: 76
  Bond restraints: 8718
  Sorted by residual:
  bond pdb=" CA  THR D  64 "
       pdb=" C   THR D  64 "
    ideal  model  delta    sigma   weight residual
    1.522  1.396  0.126 1.37e-02 5.33e+03 8.46e+01
  bond pdb=" C   LEU B 103 "
       pdb=" N   ASN B 104 "
    ideal  model  delta    sigma   weight residual
    1.331  1.203  0.129 1.40e-02 5.10e+03 8.43e+01
  bond pdb=" C   LEU B 103 "
       pdb=" O   LEU B 103 "
    ideal  model  delta    sigma   weight residual
    1.234  1.130  0.105 1.15e-02 7.56e+03 8.31e+01
  bond pdb=" CA  LEU B 103 "
       pdb=" C   LEU B 103 "
    ideal  model  delta    sigma   weight residual
    1.520  1.414  0.107 1.20e-02 6.94e+03 7.89e+01
  bond pdb=" C   CYS B 102 "
       pdb=" O   CYS B 102 "
    ideal  model  delta    sigma   weight residual
    1.235  1.133  0.103 1.26e-02 6.30e+03 6.64e+01
  ... (remaining 8713 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.26: 11388
        4.26 -     8.51: 367
        8.51 -    12.77: 45
       12.77 -    17.03: 10
       17.03 -    21.28: 6
  Bond angle restraints: 11816
  Sorted by residual:
  angle pdb=" N   PHE A 189 "
        pdb=" CA  PHE A 189 "
        pdb=" C   PHE A 189 "
      ideal   model   delta    sigma   weight residual
     113.16  130.33  -17.17 1.24e+00 6.50e-01 1.92e+02
  angle pdb=" C   ILE C   8 "
        pdb=" CA  ILE C   8 "
        pdb=" CB  ILE C   8 "
      ideal   model   delta    sigma   weight residual
     111.97   98.11   13.86 1.28e+00 6.10e-01 1.17e+02
  angle pdb=" C   MET D  71 "
        pdb=" N   LYS D  72 "
        pdb=" CA  LYS D  72 "
      ideal   model   delta    sigma   weight residual
     122.19  109.66   12.53 1.41e+00 5.03e-01 7.90e+01
  angle pdb=" C   PHE D 142 "
        pdb=" N   PRO D 143 "
        pdb=" CA  PRO D 143 "
      ideal   model   delta    sigma   weight residual
     119.84  130.64  -10.80 1.25e+00 6.40e-01 7.46e+01
  angle pdb=" C   VAL B 223 "
        pdb=" CA  VAL B 223 "
        pdb=" CB  VAL B 223 "
      ideal   model   delta    sigma   weight residual
     112.14  101.03   11.11 1.35e+00 5.49e-01 6.77e+01
  ... (remaining 11811 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4540
       17.95 -    35.89: 499
       35.89 -    53.83: 132
       53.83 -    71.78: 17
       71.78 -    89.72: 4
  Dihedral angle restraints: 5192
    sinusoidal: 2029
      harmonic: 3163
  Sorted by residual:
  dihedral pdb=" C   PHE A 183 "
           pdb=" N   PHE A 183 "
           pdb=" CA  PHE A 183 "
           pdb=" CB  PHE A 183 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -151.10   28.50     0      2.50e+00 1.60e-01 1.30e+02
  dihedral pdb=" N   PHE A 183 "
           pdb=" C   PHE A 183 "
           pdb=" CA  PHE A 183 "
           pdb=" CB  PHE A 183 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  150.73  -27.93     0      2.50e+00 1.60e-01 1.25e+02
  dihedral pdb=" N   LEU B 259 "
           pdb=" C   LEU B 259 "
           pdb=" CA  LEU B 259 "
           pdb=" CB  LEU B 259 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  143.93  -21.13     0      2.50e+00 1.60e-01 7.14e+01
  ... (remaining 5189 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.261: 1272
       0.261 -    0.522: 51
       0.522 -    0.782: 14
       0.782 -    1.043: 0
       1.043 -    1.304: 2
  Chirality restraints: 1339
  Sorted by residual:
  chirality pdb=" CA  PHE A 183 "
            pdb=" N   PHE A 183 "
            pdb=" C   PHE A 183 "
            pdb=" CB  PHE A 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.21    1.30 2.00e-01 2.50e+01 4.25e+01
  chirality pdb=" CA  LEU B 259 "
            pdb=" N   LEU B 259 "
            pdb=" C   LEU B 259 "
            pdb=" CB  LEU B 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.38    1.13 2.00e-01 2.50e+01 3.18e+01
  chirality pdb=" CG  LEU D 129 "
            pdb=" CB  LEU D 129 "
            pdb=" CD1 LEU D 129 "
            pdb=" CD2 LEU D 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.84   -0.75 2.00e-01 2.50e+01 1.41e+01
  ... (remaining 1336 not shown)

  Planarity restraints: 1486
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 186 "   -0.145 5.00e-02 4.00e+02   2.18e-01 7.59e+01
        pdb=" N   PRO A 187 "    0.377 5.00e-02 4.00e+02
        pdb=" CA  PRO A 187 "   -0.121 5.00e-02 4.00e+02
        pdb=" CD  PRO A 187 "   -0.110 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D  68 "   -0.026 2.00e-02 2.50e+03   5.02e-02 2.52e+01
        pdb=" C   PHE D  68 "    0.087 2.00e-02 2.50e+03
        pdb=" O   PHE D  68 "   -0.033 2.00e-02 2.50e+03
        pdb=" N   HIS D  69 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 229 "   -0.023 2.00e-02 2.50e+03   4.88e-02 2.38e+01
        pdb=" C   ALA B 229 "    0.084 2.00e-02 2.50e+03
        pdb=" O   ALA B 229 "   -0.033 2.00e-02 2.50e+03
        pdb=" N   GLU B 230 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 1483 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.40: 45
        2.40 -     3.03: 5810
        3.03 -     3.65: 12168
        3.65 -     4.28: 17359
        4.28 -     4.90: 30608
  Nonbonded interactions: 65990
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 314 "
            pdb=" OE1 GLN B 350 "
     model   vdw
     1.776 3.040
  nonbonded pdb=" OD1 ASP B  27 "
            pdb=" NH2 ARG B  58 "
     model   vdw
     1.869 3.120
  nonbonded pdb=" OE1 GLN B  24 "
            pdb=" CE2 PHE B  54 "
     model   vdw
     1.908 3.340
  nonbonded pdb=" O   ALA B 229 "
            pdb=" N   GLY B 231 "
     model   vdw
     1.910 3.120
  nonbonded pdb=" O   THR D  28 "
            pdb=" C   THR D  29 "
     model   vdw
     1.946 3.270
  ... (remaining 65985 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.540
  Find NCS groups from input model:        0.120
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
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      :  0.019   0.149   8718  Z= 1.235
  Angle     :  1.743  21.282  11816  Z= 1.050
  Chirality :  0.133   1.304   1339
  Planarity :  0.011   0.218   1486
  Dihedral  : 15.887  89.725   3162
  Min Nonbonded Distance : 1.776

Molprobity Statistics.
  All-atom Clashscore : 26.04
  Ramachandran Plot:
    Outliers :  1.94 %
    Allowed  : 11.10 %
    Favored  : 86.96 %
  Rotamer:
    Outliers :  8.37 %
    Allowed  :  7.28 %
    Favored  : 84.35 %
  Cbeta Deviations :  2.07 %
  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: -2.39 (0.25), residues: 1081
  helix: -0.36 (0.22), residues: 543
  sheet: -3.45 (0.48), residues: 80
  loop : -2.75 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.004   TRP D  70 
 HIS   0.019   0.003   HIS B  61 
 PHE   0.042   0.004   PHE B  20 
 TYR   0.029   0.003   TYR B 406 
 ARG   0.010   0.001   ARG B  26 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 126
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.6702 (mmt)
REVERT: A  368 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7407 (t0)
REVERT: A  388 LYS cc_start: 0.7788 (mttp) cc_final: 0.6983 (tttp)
REVERT: A  473 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7825 (ttm170)
REVERT: B   28 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7797 (m-80)
REVERT: B   90 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.6954 (t0)
REVERT: B   94 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8333 (ttpp)
REVERT: B  113 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8286 (m-80)
REVERT: B  222 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7122 (ttm170)
REVERT: D   24 PRO cc_start: 0.8738 (OUTLIER) cc_final: 0.8500 (Cg_endo)
REVERT: D   30 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7677 (t80)
REVERT: D   72 LYS cc_start: 0.9003 (mtmm) cc_final: 0.8778 (mttt)
REVERT: D  113 TYR cc_start: 0.8295 (t80) cc_final: 0.6948 (t80)
REVERT: D  122 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7336 (m-80)
REVERT: D  128 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7547 (t80)
REVERT: C    2 ASN cc_start: 0.6587 (OUTLIER) cc_final: 0.6230 (p0)
  outliers start: 77
  outliers final: 39
  residues processed: 191
  average time/residue: 0.2358
  time to fit residues: 59.8946
Evaluate side-chains
  157 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 105
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   91 HIS
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  301 SER
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  376 ASN
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  477 GLU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain B residue   28 PHE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   53 ASP
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   90 ASN
Chi-restraints excluded: chain B residue   94 LYS
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  108 TYR
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  113 PHE
Chi-restraints excluded: chain B residue  136 CYS
Chi-restraints excluded: chain B residue  200 ASN
Chi-restraints excluded: chain B residue  222 ARG
Chi-restraints excluded: chain B residue  239 TRP
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain D residue   24 PRO
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   30 TYR
Chi-restraints excluded: chain D residue   61 PHE
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue  122 TYR
Chi-restraints excluded: chain D residue  128 PHE
Chi-restraints excluded: chain D residue  130 ASN
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain C residue    2 ASN
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   40 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.9990
   chunk 80 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 365 GLN
A 375 GLN
B  61 HIS
B 195 HIS
B 200 ASN
B 214 HIS
B 227 GLN
B 279 HIS
D  84 ASN
D  97 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.140976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.116244 restraints weight = 12350.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 2.32
r_work: 0.3248 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8718  Z= 0.251
  Angle     :  0.751   9.946  11816  Z= 0.394
  Chirality :  0.047   0.185   1339
  Planarity :  0.006   0.061   1486
  Dihedral  :  9.161  58.991   1296
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  8.23 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 13.37 %
    Favored  : 81.96 %
  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: -1.30 (0.26), residues: 1081
  helix:  0.66 (0.22), residues: 561
  sheet: -2.95 (0.52), residues: 80
  loop : -2.53 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 239 
 HIS   0.006   0.001   HIS D 124 
 PHE   0.039   0.002   PHE A 183 
 TYR   0.019   0.002   TYR B  85 
 ARG   0.005   0.001   ARG A 439 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 128
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7299 (t-170)
REVERT: A  368 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.7031 (t0)
REVERT: A  473 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8008 (ttp80)
REVERT: B  107 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8507 (p)
REVERT: B  199 VAL cc_start: 0.8838 (t) cc_final: 0.8561 (p)
REVERT: D   30 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7648 (t80)
REVERT: D   92 MET cc_start: 0.8277 (mmm) cc_final: 0.7785 (tpt)
  outliers start: 43
  outliers final: 20
  residues processed: 158
  average time/residue: 0.2189
  time to fit residues: 47.4134
Evaluate side-chains
  144 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 HIS
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  376 ASN
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  477 GLU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  108 TYR
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain D residue   30 TYR
Chi-restraints excluded: chain D residue   97 GLN
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain C residue   17 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 84 optimal weight:    8.9990
   chunk 75 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0010
   chunk 36 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN
B 195 HIS
D  84 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.146792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.122449 restraints weight = 12698.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.35
r_work: 0.3330 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8718  Z= 0.191
  Angle     :  0.641   7.098  11816  Z= 0.339
  Chirality :  0.044   0.195   1339
  Planarity :  0.005   0.056   1486
  Dihedral  :  7.290  59.975   1229
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  6.29 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 16.09 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.26), residues: 1081
  helix:  1.27 (0.22), residues: 560
  sheet: -2.66 (0.50), residues: 92
  loop : -2.45 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 126 
 HIS   0.004   0.001   HIS B 214 
 PHE   0.031   0.001   PHE A 183 
 TYR   0.016   0.001   TYR D  83 
 ARG   0.005   0.000   ARG E  54 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 119
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 HIS cc_start: 0.7964 (OUTLIER) cc_final: 0.7325 (t-170)
REVERT: A  335 GLN cc_start: 0.8392 (tt0) cc_final: 0.8157 (tt0)
REVERT: A  368 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7301 (t0)
REVERT: A  413 LYS cc_start: 0.8240 (mmtm) cc_final: 0.7675 (tmtt)
REVERT: B  199 VAL cc_start: 0.8794 (t) cc_final: 0.8499 (p)
REVERT: D   30 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7682 (t80)
REVERT: D   92 MET cc_start: 0.8333 (mmm) cc_final: 0.7758 (tpt)
  outliers start: 38
  outliers final: 23
  residues processed: 147
  average time/residue: 0.2168
  time to fit residues: 43.8116
Evaluate side-chains
  136 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 HIS
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  390 MET
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  477 GLU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue   90 ASN
Chi-restraints excluded: chain B residue  108 TYR
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain D residue   30 TYR
Chi-restraints excluded: chain D residue   86 LEU
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  142 PHE
Chi-restraints excluded: chain E residue   49 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 82 optimal weight:    0.1980
   chunk 7 optimal weight:    1.9990
   chunk 60 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0670
   chunk 22 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN
B 195 HIS
D  84 ASN
D  94 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.147368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.123413 restraints weight = 12512.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.28
r_work: 0.3361 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8718  Z= 0.170
  Angle     :  0.598   7.720  11816  Z= 0.311
  Chirality :  0.042   0.164   1339
  Planarity :  0.005   0.052   1486
  Dihedral  :  6.315  58.042   1216
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.37 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 18.04 %
    Favored  : 78.59 %
  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: -0.35 (0.27), residues: 1081
  helix:  1.48 (0.23), residues: 567
  sheet: -2.04 (0.50), residues: 105
  loop : -2.28 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 239 
 HIS   0.003   0.001   HIS A 300 
 PHE   0.028   0.001   PHE A 183 
 TYR   0.014   0.001   TYR D  83 
 ARG   0.006   0.000   ARG E  54 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7211 (t-170)
REVERT: A  182 MET cc_start: 0.8201 (mmm) cc_final: 0.7487 (mmt)
REVERT: A  335 GLN cc_start: 0.8514 (tt0) cc_final: 0.8275 (tt0)
REVERT: A  388 LYS cc_start: 0.7912 (mttm) cc_final: 0.7028 (tttp)
REVERT: A  407 LYS cc_start: 0.8632 (mmtp) cc_final: 0.8123 (mttt)
REVERT: A  413 LYS cc_start: 0.8198 (mmtm) cc_final: 0.7744 (tmtt)
REVERT: B  199 VAL cc_start: 0.8703 (t) cc_final: 0.8384 (p)
REVERT: B  299 THR cc_start: 0.8510 (p) cc_final: 0.8210 (p)
REVERT: D   30 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.7657 (t80)
REVERT: D   92 MET cc_start: 0.8484 (mmm) cc_final: 0.8278 (tpt)
  outliers start: 31
  outliers final: 22
  residues processed: 150
  average time/residue: 0.2171
  time to fit residues: 44.9999
Evaluate side-chains
  142 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   91 HIS
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain A residue  390 MET
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  477 GLU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue  108 TYR
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain D residue   30 TYR
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain C residue   40 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 92 optimal weight:    0.6980
   chunk 16 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 95 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 48 optimal weight:    8.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN
D  84 ASN
D 144 ASN
C   2 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.144076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.119409 restraints weight = 12635.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 2.34
r_work: 0.3281 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   8718  Z= 0.297
  Angle     :  0.664   8.387  11816  Z= 0.344
  Chirality :  0.045   0.158   1339
  Planarity :  0.005   0.054   1486
  Dihedral  :  6.325  56.342   1212
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  7.40 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 18.37 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.26), residues: 1081
  helix:  1.34 (0.22), residues: 569
  sheet: -2.00 (0.52), residues: 93
  loop : -2.19 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 239 
 HIS   0.005   0.001   HIS B 214 
 PHE   0.033   0.002   PHE A 183 
 TYR   0.014   0.002   TYR B 274 
 ARG   0.005   0.000   ARG E  54 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 117
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7400 (t-170)
REVERT: A  182 MET cc_start: 0.8139 (mmm) cc_final: 0.7306 (mmt)
REVERT: A  335 GLN cc_start: 0.8490 (tt0) cc_final: 0.8203 (tt0)
REVERT: A  388 LYS cc_start: 0.8007 (mttm) cc_final: 0.7242 (tttp)
REVERT: A  407 LYS cc_start: 0.8490 (mmtp) cc_final: 0.8126 (mttt)
REVERT: A  413 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7721 (tmtt)
REVERT: B  199 VAL cc_start: 0.8807 (t) cc_final: 0.8528 (p)
REVERT: B  299 THR cc_start: 0.8609 (p) cc_final: 0.8279 (p)
REVERT: D   30 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.7615 (t80)
REVERT: C    6 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8367 (mtm180)
  outliers start: 42
  outliers final: 29
  residues processed: 149
  average time/residue: 0.2189
  time to fit residues: 44.7121
Evaluate side-chains
  146 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   91 HIS
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  390 MET
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  477 GLU
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue  108 TYR
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain D residue   30 TYR
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain C residue    6 ARG
Chi-restraints excluded: chain C residue   40 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 10 optimal weight:    0.4980
   chunk 102 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 103 optimal weight:    0.2980
   chunk 82 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 79 optimal weight:    3.9990
   chunk 2 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0870
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN
D  84 ASN
D 144 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.149439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.125151 restraints weight = 12443.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.31
r_work: 0.3363 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   8718  Z= 0.159
  Angle     :  0.584   9.129  11816  Z= 0.301
  Chirality :  0.042   0.162   1339
  Planarity :  0.005   0.053   1486
  Dihedral  :  5.974  52.995   1212
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.46 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 19.13 %
    Favored  : 76.74 %
  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: -0.15 (0.27), residues: 1081
  helix:  1.54 (0.23), residues: 569
  sheet: -1.91 (0.50), residues: 105
  loop : -2.03 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 239 
 HIS   0.003   0.001   HIS B 214 
 PHE   0.028   0.001   PHE A 183 
 TYR   0.013   0.001   TYR D  83 
 ARG   0.006   0.000   ARG E  54 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 125
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7262 (pm20)
REVERT: A  125 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.7364 (t-170)
REVERT: A  182 MET cc_start: 0.8133 (mmm) cc_final: 0.7890 (mmt)
REVERT: A  335 GLN cc_start: 0.8429 (tt0) cc_final: 0.8211 (tt0)
REVERT: A  388 LYS cc_start: 0.7930 (mttm) cc_final: 0.7152 (tttp)
REVERT: A  407 LYS cc_start: 0.8484 (mmtp) cc_final: 0.8189 (mttt)
REVERT: A  413 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7702 (tmtt)
REVERT: B  199 VAL cc_start: 0.8605 (t) cc_final: 0.8322 (p)
REVERT: B  299 THR cc_start: 0.8485 (p) cc_final: 0.8148 (p)
REVERT: B  417 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8093 (mm-30)
REVERT: D   30 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.7777 (t80)
REVERT: C    6 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8351 (mtm180)
  outliers start: 38
  outliers final: 26
  residues processed: 153
  average time/residue: 0.2150
  time to fit residues: 44.9271
Evaluate side-chains
  141 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 111
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   91 HIS
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  177 TYR
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  477 GLU
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue  108 TYR
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain D residue   30 TYR
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain C residue    6 ARG
Chi-restraints excluded: chain C residue   40 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0000
   chunk 51 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 97 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN
B  24 GLN
D  84 ASN
D 144 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.147971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.123330 restraints weight = 12567.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.34
r_work: 0.3338 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8718  Z= 0.189
  Angle     :  0.596   8.790  11816  Z= 0.305
  Chirality :  0.042   0.149   1339
  Planarity :  0.005   0.051   1486
  Dihedral  :  5.906  51.541   1212
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.57 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 18.91 %
    Favored  : 77.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.27), residues: 1081
  helix:  1.55 (0.23), residues: 572
  sheet: -1.88 (0.51), residues: 105
  loop : -1.98 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 239 
 HIS   0.003   0.001   HIS B 214 
 PHE   0.029   0.001   PHE A 183 
 TYR   0.019   0.001   TYR D  83 
 ARG   0.006   0.000   ARG E  54 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 114
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7232 (pm20)
REVERT: A  125 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7447 (t-170)
REVERT: A  182 MET cc_start: 0.8180 (mmm) cc_final: 0.7969 (mmt)
REVERT: A  335 GLN cc_start: 0.8470 (tt0) cc_final: 0.8223 (tt0)
REVERT: A  388 LYS cc_start: 0.7972 (mttm) cc_final: 0.7175 (tttp)
REVERT: A  407 LYS cc_start: 0.8447 (mmtp) cc_final: 0.8164 (mttt)
REVERT: A  413 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7716 (tmtt)
REVERT: B   29 PHE cc_start: 0.7372 (t80) cc_final: 0.6972 (m-80)
REVERT: B  199 VAL cc_start: 0.8683 (t) cc_final: 0.8404 (p)
REVERT: B  299 THR cc_start: 0.8498 (p) cc_final: 0.8169 (p)
REVERT: B  417 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8066 (mm-30)
REVERT: C    6 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8303 (mtm180)
  outliers start: 36
  outliers final: 30
  residues processed: 142
  average time/residue: 0.2250
  time to fit residues: 43.5291
Evaluate side-chains
  145 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   91 HIS
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  177 TYR
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  477 GLU
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  108 TYR
Chi-restraints excluded: chain B residue  234 ARG
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  279 HIS
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain C residue    6 ARG
Chi-restraints excluded: chain C residue   40 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN
D  84 ASN
D 144 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.147189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.122355 restraints weight = 12684.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.37
r_work: 0.3327 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8718  Z= 0.214
  Angle     :  0.610  10.823  11816  Z= 0.312
  Chirality :  0.043   0.149   1339
  Planarity :  0.005   0.052   1486
  Dihedral  :  5.879  52.141   1210
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.29 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 19.24 %
    Favored  : 76.74 %
  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: -0.07 (0.27), residues: 1081
  helix:  1.56 (0.22), residues: 572
  sheet: -1.76 (0.52), residues: 105
  loop : -1.97 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 239 
 HIS   0.004   0.001   HIS B 214 
 PHE   0.029   0.001   PHE A 183 
 TYR   0.018   0.001   TYR D  83 
 ARG   0.007   0.000   ARG E  54 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 115
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7278 (pm20)
REVERT: A  125 HIS cc_start: 0.7841 (OUTLIER) cc_final: 0.7459 (t-170)
REVERT: A  335 GLN cc_start: 0.8487 (tt0) cc_final: 0.8230 (tt0)
REVERT: A  388 LYS cc_start: 0.7987 (mttm) cc_final: 0.7190 (tttp)
REVERT: A  407 LYS cc_start: 0.8418 (mmtp) cc_final: 0.8135 (mttt)
REVERT: A  413 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7715 (tmtt)
REVERT: B   29 PHE cc_start: 0.7332 (t80) cc_final: 0.6931 (m-80)
REVERT: B  199 VAL cc_start: 0.8736 (t) cc_final: 0.8447 (p)
REVERT: B  299 THR cc_start: 0.8541 (p) cc_final: 0.8209 (p)
REVERT: B  417 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8067 (mm-30)
REVERT: C    6 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8284 (mtm180)
  outliers start: 37
  outliers final: 31
  residues processed: 143
  average time/residue: 0.2272
  time to fit residues: 44.1903
Evaluate side-chains
  146 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 112
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   91 HIS
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  177 TYR
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  108 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  279 HIS
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain C residue    6 ARG
Chi-restraints excluded: chain C residue   40 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 45 optimal weight:    9.9990
   chunk 86 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 80 optimal weight:    0.7980
   chunk 84 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN
D  84 ASN
D 144 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.148383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.123563 restraints weight = 12649.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.37
r_work: 0.3342 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   8718  Z= 0.182
  Angle     :  0.604  11.697  11816  Z= 0.309
  Chirality :  0.042   0.155   1339
  Planarity :  0.005   0.052   1486
  Dihedral  :  5.637  53.502   1207
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.38 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 19.46 %
    Favored  : 76.63 %
  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:  0.01 (0.27), residues: 1081
  helix:  1.65 (0.23), residues: 566
  sheet: -1.72 (0.52), residues: 105
  loop : -1.93 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 239 
 HIS   0.003   0.001   HIS B 214 
 PHE   0.031   0.001   PHE A 183 
 TYR   0.018   0.001   TYR D  83 
 ARG   0.007   0.000   ARG E  54 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 115
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7248 (pm20)
REVERT: A  125 HIS cc_start: 0.7838 (OUTLIER) cc_final: 0.7522 (t-170)
REVERT: A  388 LYS cc_start: 0.7948 (mttm) cc_final: 0.7183 (tttp)
REVERT: A  407 LYS cc_start: 0.8404 (mmtp) cc_final: 0.8174 (mttt)
REVERT: A  413 LYS cc_start: 0.8106 (mmtm) cc_final: 0.7705 (tmtt)
REVERT: B  199 VAL cc_start: 0.8694 (t) cc_final: 0.8414 (p)
REVERT: B  299 THR cc_start: 0.8488 (p) cc_final: 0.8147 (p)
REVERT: B  417 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7993 (mm-30)
REVERT: C    6 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8267 (mtm180)
  outliers start: 36
  outliers final: 28
  residues processed: 143
  average time/residue: 0.2229
  time to fit residues: 43.5139
Evaluate side-chains
  144 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   91 HIS
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  177 TYR
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  108 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  279 HIS
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain C residue    6 ARG
Chi-restraints excluded: chain C residue   40 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9990
   chunk 53 optimal weight:    8.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN
D  84 ASN
D 144 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.147560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.122739 restraints weight = 12513.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.36
r_work: 0.3331 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8718  Z= 0.206
  Angle     :  0.619  10.612  11816  Z= 0.316
  Chirality :  0.043   0.158   1339
  Planarity :  0.005   0.051   1486
  Dihedral  :  5.529  56.763   1205
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.57 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 19.67 %
    Favored  : 76.41 %
  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: -0.00 (0.27), residues: 1081
  helix:  1.58 (0.22), residues: 572
  sheet: -1.71 (0.52), residues: 105
  loop : -1.90 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 239 
 HIS   0.004   0.001   HIS B 214 
 PHE   0.033   0.002   PHE A 183 
 TYR   0.017   0.001   TYR D  83 
 ARG   0.006   0.000   ARG E  54 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 113
  time to evaluate  : 1.299 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7310 (pm20)
REVERT: A  125 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.7527 (t-170)
REVERT: A  246 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7484 (ptt-90)
REVERT: A  388 LYS cc_start: 0.7964 (mttm) cc_final: 0.7233 (tttp)
REVERT: A  413 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7677 (tmtt)
REVERT: B  199 VAL cc_start: 0.8706 (t) cc_final: 0.8427 (p)
REVERT: B  299 THR cc_start: 0.8524 (p) cc_final: 0.8183 (p)
REVERT: D   30 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.7657 (t80)
REVERT: C    6 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8230 (mtm180)
  outliers start: 36
  outliers final: 30
  residues processed: 140
  average time/residue: 0.2291
  time to fit residues: 44.5310
Evaluate side-chains
  147 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 112
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   91 HIS
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  177 TYR
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  335 GLN
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  108 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  279 HIS
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain D residue   30 TYR
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain C residue    6 ARG
Chi-restraints excluded: chain C residue   40 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 96 optimal weight:    0.3980
   chunk 105 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 ASN
D 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.149345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.125219 restraints weight = 12653.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.31
r_work: 0.3353 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8718  Z= 0.181
  Angle     :  0.618  10.946  11816  Z= 0.313
  Chirality :  0.042   0.163   1339
  Planarity :  0.005   0.052   1486
  Dihedral  :  5.463  58.610   1205
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.20 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.00 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.27), residues: 1081
  helix:  1.64 (0.23), residues: 572
  sheet: -1.74 (0.49), residues: 115
  loop : -1.84 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 239 
 HIS   0.003   0.001   HIS B 214 
 PHE   0.037   0.001   PHE A 183 
 TYR   0.018   0.001   TYR D  83 
 ARG   0.007   0.000   ARG E  54 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3374.45 seconds
wall clock time: 61 minutes 1.42 seconds (3661.42 seconds total)