Starting phenix.real_space_refine
on Thu Feb 13 23:15:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v8i_31802/02_2025/7v8i_31802_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v8i_31802/02_2025/7v8i_31802.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v8i_31802/02_2025/7v8i_31802.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v8i_31802/02_2025/7v8i_31802.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v8i_31802/02_2025/7v8i_31802_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v8i_31802/02_2025/7v8i_31802_neut.cif"
  }
  resolution = 3.6
  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=   0.077
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      47      5.16       5
     C    5956      2.51       5
     N    1651      2.21       5
     O    1726      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9388
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 2841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 396, 2841
          Classifications: {'peptide': 396}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 21, 'TRANS': 374}
          Unresolved non-hydrogen bonds: 166
          Unresolved non-hydrogen angles: 204
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 108
    Chain: "D"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1751
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 220}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "E"
      Number of atoms: 2978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 2978
          Classifications: {'peptide': 407}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 14, 'TRANS': 392}
          Unresolved non-hydrogen bonds: 171
          Unresolved non-hydrogen angles: 207
          Unresolved non-hydrogen dihedrals: 150
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 101
    Chain: "F"
      Number of atoms: 1754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1754
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 8, 'TRANS': 220}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.96, per 1000 atoms: 0.63
  Number of scatterers: 9388
  At special positions: 0
  Unit cell: (95, 86, 159, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      47     16.00
     P       6     15.00
     Mg      2     11.99
     O    1726      8.00
     N    1651      7.00
     C    5956      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.69
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2308

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 9 sheets defined
      48.8% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'C' and resid 7 through 16
    Processing helix  chain 'C' and resid 22 through 28
    Processing helix  chain 'C' and resid 28 through 59
      removed outlier: 3.764A  pdb=" N   ILE C  34 " --> pdb=" O   SER C  30 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 80
    Processing helix  chain 'C' and resid 148 through 155
    Processing helix  chain 'C' and resid 195 through 198
      removed outlier: 3.549A  pdb=" N   GLY C 198 " --> pdb=" O   GLU C 195 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 195 through 198'
    Processing helix  chain 'C' and resid 205 through 212
    Processing helix  chain 'C' and resid 233 through 237
      removed outlier: 3.824A  pdb=" N   SER C 236 " --> pdb=" O   ASP C 233 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLN C 237 " --> pdb=" O   SER C 234 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 233 through 237'
    Processing helix  chain 'C' and resid 254 through 293
      removed outlier: 3.816A  pdb=" N   GLN C 258 " --> pdb=" O   GLY C 254 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   SER C 285 " --> pdb=" O   ASN C 281 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU C 286 " --> pdb=" O   ILE C 282 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   MET C 291 " --> pdb=" O   GLY C 287 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS C 293 " --> pdb=" O   MET C 289 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 293 through 303
    Processing helix  chain 'C' and resid 306 through 335
    Processing helix  chain 'C' and resid 340 through 344
    Processing helix  chain 'C' and resid 361 through 379
    Processing helix  chain 'C' and resid 381 through 390
    Processing helix  chain 'D' and resid 48 through 56
    Processing helix  chain 'D' and resid 77 through 88
    Processing helix  chain 'D' and resid 103 through 115
      Proline residue:  D 111  - end of helix
    Processing helix  chain 'D' and resid 118 through 134
      removed outlier: 3.744A  pdb=" N   SER D 124 " --> pdb=" O   ALA D 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 142 through 146
    Processing helix  chain 'D' and resid 147 through 161
    Processing helix  chain 'D' and resid 177 through 195
    Processing helix  chain 'D' and resid 205 through 211
    Processing helix  chain 'E' and resid 11 through 17
      removed outlier: 4.169A  pdb=" N   ARG E  15 " --> pdb=" O   LEU E  11 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 27 through 60
      removed outlier: 3.601A  pdb=" N   LEU E  60 " --> pdb=" O   ASN E  56 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 77 through 87
      removed outlier: 4.254A  pdb=" N   ALA E  81 " --> pdb=" O   ASN E  77 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   LYS E  87 " --> pdb=" O   ASP E  83 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 127
    Processing helix  chain 'E' and resid 128 through 133
      removed outlier: 3.657A  pdb=" N   VAL E 133 " --> pdb=" O   LEU E 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 137 through 142
    Processing helix  chain 'E' and resid 151 through 159
      removed outlier: 5.161A  pdb=" N   ALA E 157 " --> pdb=" O   GLY E 153 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 197 through 201
      removed outlier: 3.536A  pdb=" N   HIS E 201 " --> pdb=" O   GLN E 198 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 207 through 215
    Processing helix  chain 'E' and resid 233 through 243
    Processing helix  chain 'E' and resid 258 through 294
      removed outlier: 4.044A  pdb=" N   LEU E 278 " --> pdb=" O   LEU E 274 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   MET E 293 " --> pdb=" O   SER E 289 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 296 through 305
    Processing helix  chain 'E' and resid 313 through 344
      removed outlier: 3.879A  pdb=" N   GLN E 344 " --> pdb=" O   VAL E 340 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 348 through 353
      removed outlier: 4.552A  pdb=" N   ILE E 352 " --> pdb=" O   ILE E 348 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 354 through 356
      No H-bonds generated for 'chain 'E' and resid 354 through 356'
    Processing helix  chain 'E' and resid 376 through 405
      Proline residue:  E 398  - end of helix
      removed outlier: 3.593A  pdb=" N   ILE E 405 " --> pdb=" O   ARG E 401 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 406 through 410
    Processing helix  chain 'F' and resid 48 through 56
    Processing helix  chain 'F' and resid 77 through 88
    Processing helix  chain 'F' and resid 103 through 115
      Proline residue:  F 111  - end of helix
    Processing helix  chain 'F' and resid 118 through 134
    Processing helix  chain 'F' and resid 142 through 146
    Processing helix  chain 'F' and resid 147 through 162
      removed outlier: 4.798A  pdb=" N   ASN F 162 " --> pdb=" O   ARG F 158 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 177 through 194
    Processing helix  chain 'F' and resid 205 through 211
    Processing sheet with id=AA1, first strand: chain 'C' and resid 176 through 185
      removed outlier: 11.767A  pdb=" N   GLY C 176 " --> pdb=" O   SER C 170 " (cutoff:3.500A)
      removed outlier: 9.878A  pdb=" N   SER C 170 " --> pdb=" O   GLY C 176 " (cutoff:3.500A)
      removed outlier: 9.671A  pdb=" N   ILE C 178 " --> pdb=" O   SER C 168 " (cutoff:3.500A)
      removed outlier: 8.328A  pdb=" N   SER C 168 " --> pdb=" O   ILE C 178 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER C 180 " --> pdb=" O   VAL C 166 " (cutoff:3.500A)
      removed outlier: 9.748A  pdb=" N   ASP C 100 " --> pdb=" O   PRO C 167 " (cutoff:3.500A)
      removed outlier: 11.076A  pdb=" N   ALA C 169 " --> pdb=" O   THR C  98 " (cutoff:3.500A)
      removed outlier: 15.544A  pdb=" N   THR C  98 " --> pdb=" O   ALA C 169 " (cutoff:3.500A)
      removed outlier: 22.573A  pdb=" N   GLN C 171 " --> pdb=" O   ILE C  96 " (cutoff:3.500A)
      removed outlier: 27.579A  pdb=" N   ILE C  96 " --> pdb=" O   GLN C 171 " (cutoff:3.500A)
      removed outlier: 35.076A  pdb=" N   THR C 173 " --> pdb=" O   ALA C  94 " (cutoff:3.500A)
      removed outlier: 39.560A  pdb=" N   ALA C  94 " --> pdb=" O   THR C 173 " (cutoff:3.500A)
      removed outlier: 8.380A  pdb=" N   MET C 201 " --> pdb=" O   VAL C 111 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   VAL C 113 " --> pdb=" O   MET C 201 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   VAL C 203 " --> pdb=" O   VAL C 113 " (cutoff:3.500A)
      removed outlier: 5.826A  pdb=" N   LEU C 115 " --> pdb=" O   VAL C 203 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 176 through 185
      removed outlier: 11.767A  pdb=" N   GLY C 176 " --> pdb=" O   SER C 170 " (cutoff:3.500A)
      removed outlier: 9.878A  pdb=" N   SER C 170 " --> pdb=" O   GLY C 176 " (cutoff:3.500A)
      removed outlier: 9.671A  pdb=" N   ILE C 178 " --> pdb=" O   SER C 168 " (cutoff:3.500A)
      removed outlier: 8.328A  pdb=" N   SER C 168 " --> pdb=" O   ILE C 178 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER C 180 " --> pdb=" O   VAL C 166 " (cutoff:3.500A)
      removed outlier: 9.748A  pdb=" N   ASP C 100 " --> pdb=" O   PRO C 167 " (cutoff:3.500A)
      removed outlier: 11.076A  pdb=" N   ALA C 169 " --> pdb=" O   THR C  98 " (cutoff:3.500A)
      removed outlier: 15.544A  pdb=" N   THR C  98 " --> pdb=" O   ALA C 169 " (cutoff:3.500A)
      removed outlier: 22.573A  pdb=" N   GLN C 171 " --> pdb=" O   ILE C  96 " (cutoff:3.500A)
      removed outlier: 27.579A  pdb=" N   ILE C  96 " --> pdb=" O   GLN C 171 " (cutoff:3.500A)
      removed outlier: 35.076A  pdb=" N   THR C 173 " --> pdb=" O   ALA C  94 " (cutoff:3.500A)
      removed outlier: 39.560A  pdb=" N   ALA C  94 " --> pdb=" O   THR C 173 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 129 through 130
      removed outlier: 4.188A  pdb=" N   VAL C 130 " --> pdb=" O   THR C 189 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   THR C 189 " --> pdb=" O   VAL C 130 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'D' and resid 25 through 32
      removed outlier: 7.029A  pdb=" N   HIS D  26 " --> pdb=" O   CYS D  12 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   CYS D  12 " --> pdb=" O   HIS D  26 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   VAL D  28 " --> pdb=" O   ASN D  10 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASN D  10 " --> pdb=" O   VAL D  28 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   LEU D  11 " --> pdb=" O   SER D  63 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   SER D  63 " --> pdb=" O   LEU D  11 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 89 through 92
      removed outlier: 6.439A  pdb=" N   VAL D 167 " --> pdb=" O   LEU D 200 " (cutoff:3.500A)
      removed outlier: 7.435A  pdb=" N   VAL D 202 " --> pdb=" O   VAL D 167 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA D 169 " --> pdb=" O   VAL D 202 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   GLN D 215 " --> pdb=" O   GLU D 226 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   GLU D 226 " --> pdb=" O   GLN D 215 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   GLU D 217 " --> pdb=" O   THR D 224 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 109 through 117
    Processing sheet with id=AA7, first strand: chain 'E' and resid 165 through 169
    Processing sheet with id=AA8, first strand: chain 'F' and resid 22 through 32
      removed outlier: 6.513A  pdb=" N   ASP F  23 " --> pdb=" O   TYR F  15 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   TYR F  15 " --> pdb=" O   ASP F  23 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   LEU F  11 " --> pdb=" O   ASN F  27 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   SER F  29 " --> pdb=" O   ASP F   9 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ASP F   9 " --> pdb=" O   SER F  29 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   SER F  31 " --> pdb=" O   GLN F   7 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   GLN F   7 " --> pdb=" O   SER F  31 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LEU F  11 " --> pdb=" O   SER F  63 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   SER F  63 " --> pdb=" O   LEU F  11 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 89 through 92
      removed outlier: 6.179A  pdb=" N   VAL F 167 " --> pdb=" O   LEU F 200 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   VAL F 202 " --> pdb=" O   VAL F 167 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   ALA F 169 " --> pdb=" O   VAL F 202 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   GLN F 215 " --> pdb=" O   GLU F 226 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   GLU F 226 " --> pdb=" O   GLN F 215 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   GLU F 217 " --> pdb=" O   THR F 224 " (cutoff:3.500A)

    512 hydrogen bonds defined for protein.
    1458 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: 2.76

  Time building geometry restraints manager: 3.07 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1901
        1.33 -     1.45: 2032
        1.45 -     1.57: 5510
        1.57 -     1.69: 9
        1.69 -     1.82: 90
  Bond restraints: 9542
  Sorted by residual:
  bond pdb=" O3A ANP F 302 "
       pdb=" PB  ANP F 302 "
    ideal  model  delta    sigma   weight residual
    1.700  1.554  0.146 2.00e-02 2.50e+03 5.34e+01
  bond pdb=" O3A ANP D 302 "
       pdb=" PB  ANP D 302 "
    ideal  model  delta    sigma   weight residual
    1.700  1.585  0.115 2.00e-02 2.50e+03 3.31e+01
  bond pdb=" N3B ANP F 302 "
       pdb=" PG  ANP F 302 "
    ideal  model  delta    sigma   weight residual
    1.795  1.688  0.107 2.00e-02 2.50e+03 2.85e+01
  bond pdb=" C4  ANP D 302 "
       pdb=" C5  ANP D 302 "
    ideal  model  delta    sigma   weight residual
    1.387  1.469 -0.082 2.00e-02 2.50e+03 1.70e+01
  bond pdb=" O5' ANP F 302 "
       pdb=" PA  ANP F 302 "
    ideal  model  delta    sigma   weight residual
    1.655  1.578  0.077 2.00e-02 2.50e+03 1.49e+01
  ... (remaining 9537 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.49: 12864
        3.49 -     6.99: 93
        6.99 -    10.48: 20
       10.48 -    13.98: 3
       13.98 -    17.47: 2
  Bond angle restraints: 12982
  Sorted by residual:
  angle pdb=" N   ARG E 306 "
        pdb=" CA  ARG E 306 "
        pdb=" C   ARG E 306 "
      ideal   model   delta    sigma   weight residual
     110.41  119.15   -8.74 1.23e+00 6.61e-01 5.05e+01
  angle pdb=" N   GLY F  18 "
        pdb=" CA  GLY F  18 "
        pdb=" C   GLY F  18 "
      ideal   model   delta    sigma   weight residual
     111.36  119.66   -8.30 1.17e+00 7.31e-01 5.03e+01
  angle pdb=" N   VAL C 349 "
        pdb=" CA  VAL C 349 "
        pdb=" C   VAL C 349 "
      ideal   model   delta    sigma   weight residual
     113.10  106.98    6.12 9.70e-01 1.06e+00 3.98e+01
  angle pdb=" PB  ANP F 302 "
        pdb=" N3B ANP F 302 "
        pdb=" PG  ANP F 302 "
      ideal   model   delta    sigma   weight residual
     126.95  109.48   17.47 3.00e+00 1.11e-01 3.39e+01
  angle pdb=" PB  ANP D 302 "
        pdb=" N3B ANP D 302 "
        pdb=" PG  ANP D 302 "
      ideal   model   delta    sigma   weight residual
     126.95  110.77   16.18 3.00e+00 1.11e-01 2.91e+01
  ... (remaining 12977 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.39: 5608
       35.39 -    70.79: 144
       70.79 -   106.18: 18
      106.18 -   141.57: 0
      141.57 -   176.96: 2
  Dihedral angle restraints: 5772
    sinusoidal: 2186
      harmonic: 3586
  Sorted by residual:
  dihedral pdb=" O1A ANP D 302 "
           pdb=" O3A ANP D 302 "
           pdb=" PA  ANP D 302 "
           pdb=" PB  ANP D 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -93.85  176.96     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" O1A ANP F 302 "
           pdb=" O3A ANP F 302 "
           pdb=" PA  ANP F 302 "
           pdb=" PB  ANP F 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -72.13  155.24     1      3.00e+01 1.11e-03 2.04e+01
  dihedral pdb=" CA  MET D  37 "
           pdb=" C   MET D  37 "
           pdb=" N   MET D  38 "
           pdb=" CA  MET D  38 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.86  -19.14     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 5769 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1306
       0.065 -    0.131: 223
       0.131 -    0.196: 9
       0.196 -    0.262: 5
       0.262 -    0.327: 4
  Chirality restraints: 1547
  Sorted by residual:
  chirality pdb=" CA  PRO E  74 "
            pdb=" N   PRO E  74 "
            pdb=" C   PRO E  74 "
            pdb=" CB  PRO E  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.39    0.33 2.00e-01 2.50e+01 2.68e+00
  chirality pdb=" CA  ARG E 306 "
            pdb=" N   ARG E 306 "
            pdb=" C   ARG E 306 "
            pdb=" CB  ARG E 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.33 2.00e-01 2.50e+01 2.64e+00
  chirality pdb=" CB  ILE E 280 "
            pdb=" CA  ILE E 280 "
            pdb=" CG1 ILE E 280 "
            pdb=" CG2 ILE E 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.25e+00
  ... (remaining 1544 not shown)

  Planarity restraints: 1664
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN E  73 "    0.075 5.00e-02 4.00e+02   1.11e-01 1.98e+01
        pdb=" N   PRO E  74 "   -0.192 5.00e-02 4.00e+02
        pdb=" CA  PRO E  74 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO E  74 "    0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E  95 "   -0.039 5.00e-02 4.00e+02   5.94e-02 5.65e+00
        pdb=" N   PRO E  96 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO E  96 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO E  96 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 391 "    0.033 5.00e-02 4.00e+02   4.94e-02 3.90e+00
        pdb=" N   PRO C 392 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO C 392 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 392 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1661 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 74
        2.59 -     3.16: 7945
        3.16 -     3.74: 14415
        3.74 -     4.32: 18971
        4.32 -     4.90: 30974
  Nonbonded interactions: 72379
  Sorted by model distance:
  nonbonded pdb="MG    MG F 301 "
            pdb=" O3G ANP F 302 "
     model   vdw
     2.007 2.170
  nonbonded pdb="MG    MG D 301 "
            pdb=" O3G ANP D 302 "
     model   vdw
     2.021 2.170
  nonbonded pdb="MG    MG D 301 "
            pdb=" O2B ANP D 302 "
     model   vdw
     2.059 2.170
  nonbonded pdb="MG    MG F 301 "
            pdb=" O2B ANP F 302 "
     model   vdw
     2.079 2.170
  nonbonded pdb=" O1B ANP F 302 "
            pdb=" O3G ANP F 302 "
     model   vdw
     2.081 3.040
  ... (remaining 72374 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = (chain 'F' and (resid 2 through 22 or (resid 23 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 24 through 230 or resid 301 through 302))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  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:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.640
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6019
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.146   9542  Z= 0.330
  Angle     :  0.869  17.473  12982  Z= 0.458
  Chirality :  0.050   0.327   1547
  Planarity :  0.005   0.111   1664
  Dihedral  : 15.814 176.965   3464
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.91 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  0.42 %
    Favored  : 98.22 %
  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: -0.76 (0.24), residues: 1253
  helix:  0.29 (0.22), residues: 589
  sheet: -0.19 (0.42), residues: 160
  loop : -1.51 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 246 
 HIS   0.002   0.001   HIS D  96 
 PHE   0.014   0.001   PHE E  13 
 TYR   0.009   0.001   TYR C 128 
 ARG   0.007   0.000   ARG D 138 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 197
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  344 MET cc_start: 0.1542 (tpp) cc_final: 0.1117 (tpt)
REVERT: E   68 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6435 (tp)
REVERT: E   69 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.6024 (mt-10)
REVERT: E   72 ASP cc_start: 0.4498 (OUTLIER) cc_final: 0.4091 (m-30)
REVERT: F   46 SER cc_start: 0.7564 (OUTLIER) cc_final: 0.7071 (t)
REVERT: F  147 SER cc_start: 0.8906 (p) cc_final: 0.8039 (p)
REVERT: F  182 ASP cc_start: 0.6877 (m-30) cc_final: 0.6601 (m-30)
REVERT: F  210 LYS cc_start: 0.7896 (tttp) cc_final: 0.7601 (tppt)
  outliers start: 13
  outliers final: 0
  residues processed: 206
  average time/residue: 0.2082
  time to fit residues: 60.2155
Evaluate side-chains
  159 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 155
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue   69 GLU
Chi-restraints excluded: chain E residue   72 ASP
Chi-restraints excluded: chain F residue   46 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0070
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 71 optimal weight:    9.9990
   chunk 111 optimal weight:    0.7980
   overall best weight:    0.7200

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

Flipped N/Q/H residues before XYZ refinement:
** C  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  76 ASN
C 181 GLN
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 309 GLN
E 122 GLN
** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 286 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.208540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.164006 restraints weight = 13131.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.162944 restraints weight = 8444.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.164615 restraints weight = 7111.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.092   9542  Z= 0.203
  Angle     :  0.638   7.585  12982  Z= 0.313
  Chirality :  0.045   0.251   1547
  Planarity :  0.005   0.116   1664
  Dihedral  : 11.787 172.895   1408
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.91 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.09 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.24), residues: 1253
  helix:  0.45 (0.22), residues: 597
  sheet: -0.19 (0.40), residues: 170
  loop : -1.56 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 246 
 HIS   0.002   0.000   HIS D  96 
 PHE   0.021   0.001   PHE C  51 
 TYR   0.008   0.001   TYR E 260 
 ARG   0.003   0.000   ARG C 252 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  201 MET cc_start: 0.6885 (tpp) cc_final: 0.6650 (tpp)
REVERT: C  262 MET cc_start: 0.7916 (ptm) cc_final: 0.7611 (ptp)
REVERT: D  110 MET cc_start: 0.8124 (tpp) cc_final: 0.7595 (tpp)
REVERT: E   68 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6210 (tp)
REVERT: E   69 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7077 (mp0)
REVERT: F  182 ASP cc_start: 0.7083 (m-30) cc_final: 0.6680 (m-30)
REVERT: F  212 MET cc_start: 0.6605 (ttm) cc_final: 0.6356 (ttm)
  outliers start: 18
  outliers final: 9
  residues processed: 177
  average time/residue: 0.2051
  time to fit residues: 51.7000
Evaluate side-chains
  158 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue   69 GLU
Chi-restraints excluded: chain E residue  284 CYS
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain F residue   89 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9990
   chunk 115 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 94 optimal weight:    0.0270
   chunk 45 optimal weight:    0.8980
   chunk 102 optimal weight:    0.9990
   chunk 120 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
C 181 GLN
C 294 GLN
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   7 GLN
E 122 GLN
E 201 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.208196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.163410 restraints weight = 13382.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.162849 restraints weight = 9891.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.165405 restraints weight = 7333.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6908
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.088   9542  Z= 0.188
  Angle     :  0.609  12.033  12982  Z= 0.296
  Chirality :  0.043   0.216   1547
  Planarity :  0.005   0.108   1664
  Dihedral  : 11.258 172.742   1405
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.99 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.23 %
    Favored  : 83.47 %
  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: -0.53 (0.24), residues: 1253
  helix:  0.55 (0.22), residues: 606
  sheet: -0.10 (0.41), residues: 160
  loop : -1.55 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP E  75 
 HIS   0.002   0.000   HIS E 376 
 PHE   0.009   0.001   PHE F 185 
 TYR   0.012   0.001   TYR C 199 
 ARG   0.007   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
REVERT: C  262 MET cc_start: 0.7944 (ptm) cc_final: 0.6529 (ptp)
REVERT: C  266 MET cc_start: 0.7473 (mtm) cc_final: 0.7272 (mtm)
REVERT: D  106 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7032 (mp0)
REVERT: E   68 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6147 (tp)
REVERT: E   69 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7268 (mp0)
REVERT: E  228 MET cc_start: 0.3745 (OUTLIER) cc_final: 0.3245 (mmt)
REVERT: F  182 ASP cc_start: 0.6931 (m-30) cc_final: 0.6670 (m-30)
  outliers start: 22
  outliers final: 12
  residues processed: 176
  average time/residue: 0.2366
  time to fit residues: 57.1862
Evaluate side-chains
  159 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  228 MET
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  161 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 107 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 120 optimal weight:    0.6980
   chunk 62 optimal weight:    0.4980
   chunk 84 optimal weight:    0.9990
   chunk 110 optimal weight:    4.9990
   chunk 101 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 106 optimal weight:    1.9990
   chunk 12 optimal weight:    8.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
C 161 GLN
C 218 ASN
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 137 HIS
D 163 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.204080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.158652 restraints weight = 13141.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.158154 restraints weight = 8924.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.160737 restraints weight = 7149.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   9542  Z= 0.256
  Angle     :  0.642  13.395  12982  Z= 0.310
  Chirality :  0.045   0.242   1547
  Planarity :  0.005   0.106   1664
  Dihedral  : 10.981 173.627   1402
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.15 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.74 %
    Favored  : 80.65 %
  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: -0.57 (0.24), residues: 1253
  helix:  0.44 (0.22), residues: 607
  sheet: -0.06 (0.40), residues: 166
  loop : -1.50 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 246 
 HIS   0.003   0.001   HIS D  96 
 PHE   0.014   0.001   PHE E 319 
 TYR   0.013   0.001   TYR E 258 
 ARG   0.011   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 157
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
REVERT: C  262 MET cc_start: 0.7919 (ptm) cc_final: 0.7278 (ptt)
REVERT: D  106 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6953 (mp0)
REVERT: E   68 ILE cc_start: 0.6773 (OUTLIER) cc_final: 0.5881 (tp)
REVERT: E   69 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7191 (mp0)
REVERT: E  228 MET cc_start: 0.3533 (OUTLIER) cc_final: 0.2951 (mmt)
REVERT: F  182 ASP cc_start: 0.6805 (m-30) cc_final: 0.6589 (m-30)
  outliers start: 25
  outliers final: 18
  residues processed: 172
  average time/residue: 0.2329
  time to fit residues: 55.3128
Evaluate side-chains
  167 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  228 MET
Chi-restraints excluded: chain E residue  284 CYS
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain F residue   60 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  101 ASP
Chi-restraints excluded: chain F residue  161 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 50 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 70 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0870
   chunk 67 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9980
   chunk 14 optimal weight:    9.9990
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.206388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.161135 restraints weight = 13021.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.160341 restraints weight = 8752.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.163254 restraints weight = 7120.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7006
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   9542  Z= 0.190
  Angle     :  0.609  10.904  12982  Z= 0.293
  Chirality :  0.043   0.194   1547
  Planarity :  0.004   0.103   1664
  Dihedral  : 10.589 175.526   1402
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.07 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 17.78 %
    Favored  : 79.29 %
  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: -0.43 (0.24), residues: 1253
  helix:  0.65 (0.22), residues: 593
  sheet: -0.07 (0.41), residues: 160
  loop : -1.46 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 246 
 HIS   0.002   0.000   HIS D  53 
 PHE   0.012   0.001   PHE E 319 
 TYR   0.015   0.001   TYR C 199 
 ARG   0.006   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 154
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   25 PHE cc_start: 0.6118 (OUTLIER) cc_final: 0.5384 (m-80)
REVERT: C  195 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7307 (mt-10)
REVERT: C  201 MET cc_start: 0.6779 (tpp) cc_final: 0.6492 (tpp)
REVERT: C  262 MET cc_start: 0.7893 (ptm) cc_final: 0.7612 (ptt)
REVERT: D   54 LEU cc_start: 0.8506 (tp) cc_final: 0.8169 (tp)
REVERT: D  106 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6862 (mp0)
REVERT: D  110 MET cc_start: 0.8076 (tpp) cc_final: 0.7807 (mmm)
REVERT: E   69 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7214 (mp0)
  outliers start: 28
  outliers final: 20
  residues processed: 172
  average time/residue: 0.2194
  time to fit residues: 51.7831
Evaluate side-chains
  167 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  284 CYS
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  161 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 61 optimal weight:    0.0980
   chunk 73 optimal weight:    0.9980
   chunk 18 optimal weight:   30.0000
   chunk 51 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0060
   chunk 68 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0040
   chunk 20 optimal weight:   10.0000
   chunk 91 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0870
   overall best weight:    0.1586

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

Flipped N/Q/H residues before XYZ refinement:
E 122 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.209472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.169583 restraints weight = 13289.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.166062 restraints weight = 10337.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.165960 restraints weight = 8747.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6929
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.081   9542  Z= 0.160
  Angle     :  0.598   9.399  12982  Z= 0.289
  Chirality :  0.042   0.190   1547
  Planarity :  0.004   0.101   1664
  Dihedral  : 10.205 177.714   1402
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.59 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.67 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.24), residues: 1253
  helix:  0.92 (0.22), residues: 584
  sheet: -0.06 (0.42), residues: 160
  loop : -1.53 (0.26), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 246 
 HIS   0.003   0.000   HIS D  53 
 PHE   0.009   0.001   PHE F 185 
 TYR   0.013   0.001   TYR F  15 
 ARG   0.006   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 PHE cc_start: 0.6131 (OUTLIER) cc_final: 0.5292 (m-80)
REVERT: C  201 MET cc_start: 0.6867 (tpp) cc_final: 0.6589 (tpp)
REVERT: C  262 MET cc_start: 0.7827 (ptm) cc_final: 0.7607 (ptt)
REVERT: D  106 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6802 (mp0)
REVERT: D  110 MET cc_start: 0.8012 (tpp) cc_final: 0.7790 (mmm)
REVERT: E   55 LEU cc_start: 0.8470 (tt) cc_final: 0.8232 (tt)
  outliers start: 22
  outliers final: 13
  residues processed: 169
  average time/residue: 0.2189
  time to fit residues: 51.3755
Evaluate side-chains
  162 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 147
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  276 MET
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain F residue   66 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 77 optimal weight:    8.9990
   chunk 101 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0010
   chunk 86 optimal weight:    3.9990
   chunk 16 optimal weight:   20.0000
   chunk 87 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 9 optimal weight:    6.9990
   overall best weight:    1.3592

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

Flipped N/Q/H residues before XYZ refinement:
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.204554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.160369 restraints weight = 13347.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.158212 restraints weight = 8862.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.159526 restraints weight = 7423.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   9542  Z= 0.248
  Angle     :  0.638   8.227  12982  Z= 0.309
  Chirality :  0.045   0.225   1547
  Planarity :  0.005   0.098   1664
  Dihedral  : 10.234 176.506   1402
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.47 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 20.92 %
    Favored  : 76.46 %
  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: -0.45 (0.24), residues: 1253
  helix:  0.69 (0.22), residues: 592
  sheet: -0.11 (0.41), residues: 160
  loop : -1.54 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  75 
 HIS   0.002   0.001   HIS E 376 
 PHE   0.030   0.002   PHE E 203 
 TYR   0.016   0.001   TYR C 199 
 ARG   0.007   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 145
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 PHE cc_start: 0.6051 (OUTLIER) cc_final: 0.5238 (m-80)
REVERT: C  262 MET cc_start: 0.7864 (ptm) cc_final: 0.7534 (ptt)
REVERT: D   54 LEU cc_start: 0.8563 (tp) cc_final: 0.8224 (tp)
REVERT: D  106 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6885 (mp0)
REVERT: D  110 MET cc_start: 0.8109 (tpp) cc_final: 0.7867 (mmm)
REVERT: E   48 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6943 (ttp)
  outliers start: 25
  outliers final: 18
  residues processed: 161
  average time/residue: 0.2232
  time to fit residues: 50.5922
Evaluate side-chains
  163 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 142
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   48 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  228 MET
Chi-restraints excluded: chain E residue  284 CYS
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  390 LEU
Chi-restraints excluded: chain F residue    8 CYS
Chi-restraints excluded: chain F residue   66 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 36 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 70 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   chunk 116 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   chunk 29 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 79 optimal weight:   30.0000
   chunk 96 optimal weight:    0.6980
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.204297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.158626 restraints weight = 13511.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.158053 restraints weight = 9195.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.160657 restraints weight = 7048.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   9542  Z= 0.235
  Angle     :  0.632   9.560  12982  Z= 0.306
  Chirality :  0.044   0.228   1547
  Planarity :  0.004   0.095   1664
  Dihedral  : 10.237 176.905   1402
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.39 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 21.65 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.24), residues: 1253
  helix:  0.65 (0.22), residues: 592
  sheet: -0.14 (0.42), residues: 160
  loop : -1.53 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  75 
 HIS   0.002   0.001   HIS D  96 
 PHE   0.024   0.001   PHE E 203 
 TYR   0.013   0.001   TYR F  15 
 ARG   0.005   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 143
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 PHE cc_start: 0.6111 (OUTLIER) cc_final: 0.5280 (m-80)
REVERT: C  262 MET cc_start: 0.7987 (ptm) cc_final: 0.7596 (ptt)
REVERT: D   54 LEU cc_start: 0.8591 (tp) cc_final: 0.8257 (tp)
REVERT: D  106 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6931 (mp0)
REVERT: D  110 MET cc_start: 0.8190 (tpp) cc_final: 0.7884 (mmm)
REVERT: D  212 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7146 (mpt)
REVERT: E   55 LEU cc_start: 0.8539 (tt) cc_final: 0.8211 (tt)
  outliers start: 27
  outliers final: 19
  residues processed: 161
  average time/residue: 0.2233
  time to fit residues: 49.6108
Evaluate side-chains
  163 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  284 CYS
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  390 LEU
Chi-restraints excluded: chain F residue    8 CYS
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  101 ASP
Chi-restraints excluded: chain F residue  147 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 56 optimal weight:    0.0470
   chunk 85 optimal weight:    0.9980
   chunk 105 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0570
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 109 optimal weight:    0.6980
   chunk 110 optimal weight:    0.6980
   chunk 41 optimal weight:    4.9990
   chunk 98 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 171 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.206950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.164157 restraints weight = 13288.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.162681 restraints weight = 8888.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.162848 restraints weight = 6925.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6987
moved from start:          0.2767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   9542  Z= 0.178
  Angle     :  0.619  12.176  12982  Z= 0.298
  Chirality :  0.043   0.196   1547
  Planarity :  0.004   0.093   1664
  Dihedral  : 10.122 178.200   1402
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.99 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 22.59 %
    Favored  : 75.10 %
  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: -0.31 (0.24), residues: 1253
  helix:  0.86 (0.22), residues: 591
  sheet: -0.10 (0.42), residues: 160
  loop : -1.52 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 246 
 HIS   0.002   0.000   HIS D  53 
 PHE   0.022   0.001   PHE F  68 
 TYR   0.018   0.001   TYR C 199 
 ARG   0.007   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 PHE cc_start: 0.6072 (OUTLIER) cc_final: 0.5188 (m-80)
REVERT: C  156 VAL cc_start: 0.3874 (OUTLIER) cc_final: 0.3577 (m)
REVERT: D   54 LEU cc_start: 0.8482 (tp) cc_final: 0.8183 (tp)
REVERT: D  106 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7081 (mp0)
REVERT: D  110 MET cc_start: 0.8130 (tpp) cc_final: 0.7887 (mmm)
REVERT: D  212 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7161 (mpt)
REVERT: E   55 LEU cc_start: 0.8504 (tt) cc_final: 0.8145 (tt)
  outliers start: 22
  outliers final: 16
  residues processed: 169
  average time/residue: 0.2223
  time to fit residues: 52.3240
Evaluate side-chains
  167 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  390 LEU
Chi-restraints excluded: chain F residue    8 CYS
Chi-restraints excluded: chain F residue   66 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 43 optimal weight:    6.9990
   chunk 110 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 50 optimal weight:    0.1980
   chunk 102 optimal weight:    0.2980
   chunk 32 optimal weight:    0.8980
   chunk 118 optimal weight:    0.1980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.207389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.163776 restraints weight = 13395.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.161477 restraints weight = 9472.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.163299 restraints weight = 7830.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6995
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   9542  Z= 0.180
  Angle     :  0.621  12.743  12982  Z= 0.297
  Chirality :  0.043   0.186   1547
  Planarity :  0.004   0.091   1664
  Dihedral  : 10.057 179.358   1402
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.31 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 23.12 %
    Favored  : 74.79 %
  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: -0.18 (0.24), residues: 1253
  helix:  0.94 (0.22), residues: 587
  sheet:  0.04 (0.43), residues: 160
  loop : -1.45 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 246 
 HIS   0.002   0.000   HIS D 204 
 PHE   0.019   0.001   PHE E 203 
 TYR   0.010   0.001   TYR E 258 
 ARG   0.005   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 157
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 PHE cc_start: 0.5947 (OUTLIER) cc_final: 0.5044 (m-80)
REVERT: D   54 LEU cc_start: 0.8166 (tp) cc_final: 0.7900 (tp)
REVERT: D  106 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7066 (mp0)
REVERT: D  110 MET cc_start: 0.8092 (tpp) cc_final: 0.7852 (mmm)
REVERT: D  212 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7265 (mpt)
REVERT: E   55 LEU cc_start: 0.8463 (tt) cc_final: 0.8079 (tt)
REVERT: E  276 MET cc_start: 0.4502 (mmp) cc_final: 0.3909 (ptt)
REVERT: E  296 LYS cc_start: 0.7591 (tmtt) cc_final: 0.6977 (ttmt)
  outliers start: 20
  outliers final: 16
  residues processed: 172
  average time/residue: 0.2218
  time to fit residues: 53.2553
Evaluate side-chains
  163 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  390 LEU
Chi-restraints excluded: chain F residue    8 CYS
Chi-restraints excluded: chain F residue   66 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 10 optimal weight:   20.0000
   chunk 65 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9980
   chunk 60 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0040
   overall best weight:    0.9796

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

Flipped N/Q/H residues before XYZ refinement:
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.205787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.162415 restraints weight = 13352.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.159629 restraints weight = 10682.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.161586 restraints weight = 7962.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.2965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   9542  Z= 0.216
  Angle     :  0.635  12.556  12982  Z= 0.305
  Chirality :  0.043   0.199   1547
  Planarity :  0.004   0.089   1664
  Dihedral  : 10.115 179.073   1402
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.23 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 23.54 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.24), residues: 1253
  helix:  0.82 (0.22), residues: 590
  sheet: -0.01 (0.42), residues: 160
  loop : -1.40 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 246 
 HIS   0.002   0.000   HIS D  96 
 PHE   0.009   0.001   PHE E 319 
 TYR   0.016   0.001   TYR C 199 
 ARG   0.005   0.000   ARG C 261 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2887.46 seconds
wall clock time: 52 minutes 30.13 seconds (3150.13 seconds total)