Starting phenix.real_space_refine
on Sun Jul 27 15:54:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v8i_31802/07_2025/7v8i_31802_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v8i_31802/07_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_31802/07_2025/7v8i_31802.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v8i_31802/07_2025/7v8i_31802.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v8i_31802/07_2025/7v8i_31802_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v8i_31802/07_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.59, per 1000 atoms: 0.70
  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: 3.54
  Conformation dependent library (CDL) restraints added in 1.5 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: 1.03
  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: 2.73

  Time building geometry restraints manager: 4.01 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:             2.360
  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:          0.560
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     27.960
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.070
  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:3.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.340
-------------------------------------------------------------------------------
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= 0.250
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12782 (  503)
  hydrogen bonds       : angle       6.17404 ( 1458)
  covalent geometry    : bond        0.00489 ( 9542)
  covalent geometry    : angle       0.86866 (12982)

*********************** 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  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  344 MET cc_start: 0.1542 (tpp) cc_final: 0.1118 (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: 0.6025 (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: 0.8300 (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: 0.7602 (tppt)
  outliers start: 13
  outliers final: 0
  residues processed: 206
  average time/residue: 0.2197
  time to fit residues: 64.0436
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  : 1.018 
-------------------------------------------------------------------------------
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 = 0.4532 r_free = 0.4532 target = 0.208690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.164788 restraints weight = 13203.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.162700 restraints weight = 9572.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.164382 restraints weight = 7239.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
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   0.088   9542  Z= 0.133
  Angle     :  0.638   7.567  12982  Z= 0.313
  Chirality :  0.045   0.253   1547
  Planarity :  0.005   0.117   1664
  Dihedral  : 11.638 173.276   1408
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.91 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 11.19 %
    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:  0.46 (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   0.020   0.001   PHE C  51 
 TYR   0.009   0.001   TYR E 260 
 ARG   0.003   0.000   ARG C 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03793 (  503)
  hydrogen bonds       : angle       5.09718 ( 1458)
  covalent geometry    : bond        0.00306 ( 9542)
  covalent geometry    : angle       0.63826 (12982)

*********************** 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
  183 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  201 MET cc_start: 0.6998 (tpp) cc_final: 0.6780 (tpp)
REVERT: C  262 MET cc_start: 0.7910 (ptm) cc_final: 0.7591 (ptp)
REVERT: E   68 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6231 (tp)
REVERT: E   69 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7112 (mp0)
REVERT: F  182 ASP cc_start: 0.7037 (m-30) cc_final: 0.6647 (m-30)
REVERT: F  212 MET cc_start: 0.6596 (ttm) cc_final: 0.6364 (ttm)
  outliers start: 17
  outliers final: 9
  residues processed: 176
  average time/residue: 0.2011
  time to fit residues: 50.1526
Evaluate side-chains
  156 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
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  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 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:   10.0000
   chunk 103 optimal weight:    0.9990
   chunk 115 optimal weight:    0.1980
   chunk 37 optimal weight:    0.7980
   chunk 84 optimal weight:    0.5980
   chunk 52 optimal weight:    4.9990
   chunk 94 optimal weight:    0.0770
   chunk 45 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
C 161 GLN
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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.208311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.163960 restraints weight = 13372.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.163104 restraints weight = 9077.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.164057 restraints weight = 7012.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087   9542  Z= 0.119
  Angle     :  0.605  11.195  12982  Z= 0.295
  Chirality :  0.043   0.221   1547
  Planarity :  0.005   0.108   1664
  Dihedral  : 11.023 172.721   1405
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.07 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.02 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.24), residues: 1253
  helix:  0.59 (0.22), residues: 603
  sheet: -0.11 (0.41), residues: 160
  loop : -1.55 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E  75 
 HIS   0.003   0.000   HIS E 376 
 PHE   0.009   0.001   PHE E 319 
 TYR   0.012   0.001   TYR C 199 
 ARG   0.007   0.000   ARG C 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03542 (  503)
  hydrogen bonds       : angle       4.85854 ( 1458)
  covalent geometry    : bond        0.00277 ( 9542)
  covalent geometry    : angle       0.60540 (12982)

*********************** 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
  189 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 163
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
REVERT: C  262 MET cc_start: 0.7956 (ptm) cc_final: 0.6457 (ptp)
REVERT: D  106 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7043 (mp0)
REVERT: E   68 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.6145 (tp)
REVERT: E  228 MET cc_start: 0.3749 (OUTLIER) cc_final: 0.3227 (mmt)
REVERT: F  182 ASP cc_start: 0.7067 (m-30) cc_final: 0.6800 (m-30)
  outliers start: 26
  outliers final: 14
  residues processed: 181
  average time/residue: 0.2198
  time to fit residues: 54.8578
Evaluate side-chains
  163 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
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   59 ASP
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 E residue  325 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:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 120 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 110 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 106 optimal weight:    1.9990
   chunk 12 optimal weight:    9.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.6786

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.203398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.157965 restraints weight = 13063.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.156623 restraints weight = 8793.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.157946 restraints weight = 6958.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
moved from start:          0.2014

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= 0.179
  Angle     :  0.666  13.501  12982  Z= 0.322
  Chirality :  0.046   0.252   1547
  Planarity :  0.005   0.107   1664
  Dihedral  : 10.780 173.529   1402
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.31 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.95 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.24), residues: 1253
  helix:  0.35 (0.21), residues: 601
  sheet: -0.08 (0.40), residues: 166
  loop : -1.45 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E  75 
 HIS   0.003   0.001   HIS D  96 
 PHE   0.015   0.001   PHE E 319 
 TYR   0.011   0.001   TYR E 258 
 ARG   0.007   0.000   ARG C 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03752 (  503)
  hydrogen bonds       : angle       4.89680 ( 1458)
  covalent geometry    : bond        0.00424 ( 9542)
  covalent geometry    : angle       0.66631 (12982)

*********************** 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
  180 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 1.418 
Fit side-chains
   revert: symmetry clash
REVERT: C  262 MET cc_start: 0.7976 (ptm) cc_final: 0.7663 (ptt)
REVERT: D  106 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6996 (mp0)
REVERT: E   68 ILE cc_start: 0.6830 (OUTLIER) cc_final: 0.6065 (tp)
REVERT: E   69 GLU cc_start: 0.7171 (mp0) cc_final: 0.6960 (mp0)
REVERT: E  228 MET cc_start: 0.3654 (OUTLIER) cc_final: 0.3044 (mmt)
REVERT: F  182 ASP cc_start: 0.7031 (m-30) cc_final: 0.6752 (m-30)
  outliers start: 29
  outliers final: 20
  residues processed: 169
  average time/residue: 0.2491
  time to fit residues: 58.7179
Evaluate side-chains
  169 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  147 SER
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:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 70 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 105 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 98 optimal weight:    0.8980
   chunk 14 optimal weight:    9.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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**
D 163 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.205863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.160587 restraints weight = 13004.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.160003 restraints weight = 8775.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.162365 restraints weight = 6986.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   9542  Z= 0.123
  Angle     :  0.609  11.161  12982  Z= 0.294
  Chirality :  0.043   0.204   1547
  Planarity :  0.004   0.103   1664
  Dihedral  : 10.371 175.230   1402
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.31 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 18.31 %
    Favored  : 78.97 %
  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: -0.44 (0.24), residues: 1253
  helix:  0.59 (0.22), residues: 594
  sheet: -0.03 (0.41), residues: 166
  loop : -1.45 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 246 
 HIS   0.002   0.000   HIS D  96 
 PHE   0.012   0.001   PHE E 319 
 TYR   0.015   0.001   TYR C 199 
 ARG   0.006   0.000   ARG C 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03455 (  503)
  hydrogen bonds       : angle       4.73865 ( 1458)
  covalent geometry    : bond        0.00288 ( 9542)
  covalent geometry    : angle       0.60940 (12982)

*********************** 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
  179 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 153
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
REVERT: C  195 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7302 (mt-10)
REVERT: C  262 MET cc_start: 0.7898 (ptm) cc_final: 0.7609 (ptt)
REVERT: D   54 LEU cc_start: 0.8548 (tp) cc_final: 0.8224 (tp)
REVERT: D  106 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6905 (mp0)
REVERT: D  110 MET cc_start: 0.8096 (tpp) cc_final: 0.7818 (mmm)
REVERT: E   69 GLU cc_start: 0.7005 (mp0) cc_final: 0.6796 (mp0)
REVERT: E  228 MET cc_start: 0.3429 (OUTLIER) cc_final: 0.2819 (mmt)
  outliers start: 26
  outliers final: 17
  residues processed: 169
  average time/residue: 0.2249
  time to fit residues: 52.8462
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  : 1.065 
-------------------------------------------------------------------------------
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  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  228 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
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:    0.4980
   chunk 73 optimal weight:    0.9980
   chunk 18 optimal weight:   30.0000
   chunk 51 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 34 optimal weight:    0.1980
   chunk 20 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 102 optimal weight:    0.2980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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**
E 122 GLN
F 192 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.206709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.164627 restraints weight = 13237.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.162089 restraints weight = 9159.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.162344 restraints weight = 7289.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080   9542  Z= 0.117
  Angle     :  0.603   8.989  12982  Z= 0.293
  Chirality :  0.043   0.190   1547
  Planarity :  0.004   0.101   1664
  Dihedral  : 10.089 176.679   1402
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.15 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.35 %
    Favored  : 78.35 %
  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: -0.37 (0.24), residues: 1253
  helix:  0.77 (0.22), residues: 586
  sheet: -0.05 (0.42), residues: 160
  loop : -1.50 (0.27), residues: 507

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   0.010   0.001   PHE E 319 
 TYR   0.012   0.001   TYR F  15 
 ARG   0.008   0.000   ARG C 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03420 (  503)
  hydrogen bonds       : angle       4.69353 ( 1458)
  covalent geometry    : bond        0.00276 ( 9542)
  covalent geometry    : angle       0.60286 (12982)

*********************** 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
  174 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
REVERT: C  201 MET cc_start: 0.6909 (tpp) cc_final: 0.6571 (tpp)
REVERT: C  262 MET cc_start: 0.7993 (ptm) cc_final: 0.7753 (ptt)
REVERT: D   54 LEU cc_start: 0.8549 (tp) cc_final: 0.8187 (tp)
REVERT: D  106 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6902 (mp0)
REVERT: D  110 MET cc_start: 0.8110 (tpp) cc_final: 0.7856 (mmm)
REVERT: E   55 LEU cc_start: 0.8502 (tt) cc_final: 0.8259 (tt)
REVERT: E  390 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.5876 (tp)
  outliers start: 22
  outliers final: 15
  residues processed: 165
  average time/residue: 0.2137
  time to fit residues: 49.1172
Evaluate side-chains
  164 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
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  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  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   66 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 101 optimal weight:    3.9990
   chunk 97 optimal weight:    7.9990
   chunk 86 optimal weight:    9.9990
   chunk 16 optimal weight:   30.0000
   chunk 87 optimal weight:    0.9980
   chunk 113 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 9 optimal weight:   20.0000
   overall best weight:    2.1784

-------------------------------------------------------------------------------
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 = 0.4442 r_free = 0.4442 target = 0.199703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.156651 restraints weight = 13283.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.153590 restraints weight = 12057.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.155333 restraints weight = 10356.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7063
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   9542  Z= 0.215
  Angle     :  0.707   8.903  12982  Z= 0.344
  Chirality :  0.047   0.252   1547
  Planarity :  0.005   0.098   1664
  Dihedral  : 10.195 178.439   1402
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.11 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 20.71 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.24), residues: 1253
  helix:  0.33 (0.21), residues: 595
  sheet: -0.18 (0.41), residues: 166
  loop : -1.57 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP E  75 
 HIS   0.004   0.001   HIS D  96 
 PHE   0.014   0.002   PHE E 319 
 TYR   0.019   0.002   TYR F  15 
 ARG   0.007   0.001   ARG C 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03984 (  503)
  hydrogen bonds       : angle       5.02580 ( 1458)
  covalent geometry    : bond        0.00507 ( 9542)
  covalent geometry    : angle       0.70721 (12982)

*********************** 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
  181 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 150
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
REVERT: C   24 ARG cc_start: 0.7069 (ptt180) cc_final: 0.6854 (ttp80)
REVERT: C   25 PHE cc_start: 0.6110 (OUTLIER) cc_final: 0.5240 (m-80)
REVERT: C  261 ARG cc_start: 0.8749 (mmp-170) cc_final: 0.8452 (mmp-170)
REVERT: C  262 MET cc_start: 0.7883 (ptm) cc_final: 0.7618 (ptt)
REVERT: D  106 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7064 (mp0)
REVERT: D  212 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7249 (mpt)
REVERT: E  305 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.5841 (pt)
REVERT: E  390 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6065 (tp)
  outliers start: 31
  outliers final: 24
  residues processed: 168
  average time/residue: 0.2654
  time to fit residues: 60.8308
Evaluate side-chains
  171 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 142
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
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   42 VAL
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  316 VAL
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain C residue  397 ARG
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  279 VAL
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   60 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  101 ASP
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:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 70 optimal weight:   20.0000
   chunk 5 optimal weight:    3.9990
   chunk 116 optimal weight:    0.6980
   chunk 72 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 79 optimal weight:   30.0000
   chunk 96 optimal weight:    0.5980
   overall best weight:    1.4382

-------------------------------------------------------------------------------
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 = 0.4462 r_free = 0.4462 target = 0.201643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.159867 restraints weight = 13363.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.156331 restraints weight = 12252.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.158244 restraints weight = 9793.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   9542  Z= 0.164
  Angle     :  0.656   8.954  12982  Z= 0.321
  Chirality :  0.045   0.225   1547
  Planarity :  0.004   0.094   1664
  Dihedral  : 10.128 179.207   1402
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.87 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 22.07 %
    Favored  : 74.90 %
  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:  0.46 (0.22), residues: 588
  sheet: -0.13 (0.41), residues: 166
  loop : -1.54 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  75 
 HIS   0.002   0.001   HIS D  96 
 PHE   0.015   0.001   PHE E 203 
 TYR   0.015   0.001   TYR F  15 
 ARG   0.004   0.000   ARG C 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03724 (  503)
  hydrogen bonds       : angle       4.89595 ( 1458)
  covalent geometry    : bond        0.00386 ( 9542)
  covalent geometry    : angle       0.65583 (12982)

*********************** 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
  176 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 1.390 
Fit side-chains
   revert: symmetry clash
REVERT: C   24 ARG cc_start: 0.7053 (ptt180) cc_final: 0.6741 (ttp80)
REVERT: C   25 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.5274 (m-80)
REVERT: C  262 MET cc_start: 0.7920 (ptm) cc_final: 0.7430 (ptt)
REVERT: D  106 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6977 (mp0)
REVERT: D  212 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7277 (mpt)
REVERT: E   52 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6151 (mp0)
REVERT: F  147 SER cc_start: 0.8715 (OUTLIER) cc_final: 0.8280 (t)
  outliers start: 29
  outliers final: 20
  residues processed: 166
  average time/residue: 0.2658
  time to fit residues: 60.2316
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  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   45 LEU
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 C residue  397 ARG
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   52 GLU
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   60 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  147 SER
Chi-restraints excluded: chain F residue  150 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 56 optimal weight:    0.1980
   chunk 85 optimal weight:    8.9990
   chunk 105 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 23 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 109 optimal weight:    0.0020
   chunk 110 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 98 optimal weight:    0.4980
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.5188

-------------------------------------------------------------------------------
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 = 0.4492 r_free = 0.4492 target = 0.204738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.160454 restraints weight = 13258.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.159626 restraints weight = 8931.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.160433 restraints weight = 7586.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.2865

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= 0.119
  Angle     :  0.626   9.172  12982  Z= 0.305
  Chirality :  0.043   0.189   1547
  Planarity :  0.004   0.092   1664
  Dihedral  : 10.006 177.098   1402
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.79 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 22.18 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.24), residues: 1253
  helix:  0.73 (0.22), residues: 584
  sheet: -0.18 (0.42), residues: 160
  loop : -1.45 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 246 
 HIS   0.002   0.000   HIS D  96 
 PHE   0.012   0.001   PHE E  13 
 TYR   0.017   0.001   TYR C 199 
 ARG   0.007   0.000   ARG C 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03451 (  503)
  hydrogen bonds       : angle       4.75261 ( 1458)
  covalent geometry    : bond        0.00280 ( 9542)
  covalent geometry    : angle       0.62600 (12982)

*********************** 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
  178 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 1.553 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 PHE cc_start: 0.6174 (OUTLIER) cc_final: 0.5312 (m-80)
REVERT: C  262 MET cc_start: 0.7946 (ptm) cc_final: 0.7738 (ptt)
REVERT: D  106 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6913 (mp0)
REVERT: D  110 MET cc_start: 0.8022 (tpp) cc_final: 0.7361 (tpp)
REVERT: D  212 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7219 (mpt)
REVERT: E   52 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6072 (mp0)
REVERT: E   55 LEU cc_start: 0.8540 (tt) cc_final: 0.8169 (tt)
REVERT: F  147 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8187 (t)
  outliers start: 27
  outliers final: 19
  residues processed: 169
  average time/residue: 0.2464
  time to fit residues: 58.4780
Evaluate side-chains
  172 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 1.736 
-------------------------------------------------------------------------------
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  288 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  316 VAL
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain C residue  397 ARG
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  171 GLN
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   52 GLU
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   66 VAL
Chi-restraints excluded: chain F residue  147 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 43 optimal weight:    6.9990
   chunk 110 optimal weight:    0.0030
   chunk 72 optimal weight:    8.9990
   chunk 4 optimal weight:    5.9990
   chunk 50 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.6590

-------------------------------------------------------------------------------
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 = 0.204196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.160282 restraints weight = 13339.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.158627 restraints weight = 9543.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.160416 restraints weight = 7602.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.2916

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= 0.124
  Angle     :  0.627   8.927  12982  Z= 0.306
  Chirality :  0.043   0.187   1547
  Planarity :  0.004   0.090   1664
  Dihedral  :  9.989 177.364   1402
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.87 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 22.07 %
    Favored  : 75.21 %
  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: -0.37 (0.24), residues: 1253
  helix:  0.76 (0.22), residues: 584
  sheet: -0.12 (0.42), residues: 160
  loop : -1.45 (0.27), residues: 509

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   0.021   0.001   PHE E 203 
 TYR   0.011   0.001   TYR E 258 
 ARG   0.004   0.000   ARG C 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03435 (  503)
  hydrogen bonds       : angle       4.71639 ( 1458)
  covalent geometry    : bond        0.00292 ( 9542)
  covalent geometry    : angle       0.62684 (12982)

********************** 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
  178 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 PHE cc_start: 0.6178 (OUTLIER) cc_final: 0.5273 (m-80)
REVERT: C  201 MET cc_start: 0.6915 (tpp) cc_final: 0.6612 (mmm)
REVERT: C  282 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7226 (mt)
REVERT: D  106 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6860 (mp0)
REVERT: D  110 MET cc_start: 0.8018 (tpp) cc_final: 0.7361 (tpp)
REVERT: D  212 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7220 (mpt)
REVERT: E   52 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6145 (mp0)
REVERT: E   55 LEU cc_start: 0.8554 (tt) cc_final: 0.8166 (tt)
REVERT: F  147 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8217 (t)
  outliers start: 26
  outliers final: 18
  residues processed: 169
  average time/residue: 0.2212
  time to fit residues: 51.7177
Evaluate side-chains
  172 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
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  282 ILE
Chi-restraints excluded: chain C residue  288 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  316 VAL
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   52 GLU
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 F residue   66 VAL
Chi-restraints excluded: chain F residue  147 SER
Chi-restraints excluded: chain F residue  216 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 92 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 101 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 99 optimal weight:    0.6980
   chunk 60 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0170
   overall best weight:    0.6218

-------------------------------------------------------------------------------
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**
** F 152 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 = 0.4495 r_free = 0.4495 target = 0.204869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.160143 restraints weight = 13314.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.159373 restraints weight = 9104.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.161461 restraints weight = 7446.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.2962

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= 0.122
  Angle     :  0.624   9.029  12982  Z= 0.304
  Chirality :  0.043   0.237   1547
  Planarity :  0.004   0.088   1664
  Dihedral  :  9.971 178.508   1402
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.47 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 22.18 %
    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: -0.30 (0.24), residues: 1253
  helix:  0.83 (0.22), residues: 582
  sheet: -0.09 (0.42), residues: 160
  loop : -1.43 (0.27), residues: 511

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   0.024   0.001   PHE F  68 
 TYR   0.017   0.001   TYR C 199 
 ARG   0.004   0.000   ARG C 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03425 (  503)
  hydrogen bonds       : angle       4.65462 ( 1458)
  covalent geometry    : bond        0.00287 ( 9542)
  covalent geometry    : angle       0.62424 (12982)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3215.61 seconds
wall clock time: 57 minutes 53.51 seconds (3473.51 seconds total)