Starting phenix.real_space_refine
on Fri Aug 22 21:01:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w6i_37324/08_2025/8w6i_37324.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w6i_37324/08_2025/8w6i_37324.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w6i_37324/08_2025/8w6i_37324.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w6i_37324/08_2025/8w6i_37324.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w6i_37324/08_2025/8w6i_37324.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w6i_37324/08_2025/8w6i_37324.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      34      5.16       5
     C    4949      2.51       5
     N    1349      2.21       5
     O    1412      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7750
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1637
          Classifications: {'peptide': 217}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 7, 'TRANS': 209}
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 40
          Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "C"
      Number of atoms: 2204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2204
          Classifications: {'peptide': 292}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 9, 'TRANS': 282}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'TRP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "D"
      Number of atoms: 1673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1673
          Classifications: {'peptide': 219}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 2174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2174
          Classifications: {'peptide': 293}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 9, 'TRANS': 283}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 95
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'ARG:plan': 4, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 55
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'AGS': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'AGS': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.10, per 1000 atoms: 0.27
  Number of scatterers: 7750
  At special positions: 0
  Unit cell: (63.6, 81.62, 148.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     P       6     15.00
     O    1412      8.00
     N    1349      7.00
     C    4949      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: 0.64
  Conformation dependent library (CDL) restraints added in 415.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1864

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 6 sheets defined
      58.0% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'B' and resid 41 through 48
      removed outlier: 3.850A  pdb=" N   ILE B  48 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 78
    Processing helix  chain 'B' and resid 79 through 81
      No H-bonds generated for 'chain 'B' and resid 79 through 81'
    Processing helix  chain 'B' and resid 95 through 99
      removed outlier: 3.604A  pdb=" N   ASP B  98 " --> pdb=" O   THR B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 108
    Processing helix  chain 'B' and resid 110 through 112
      No H-bonds generated for 'chain 'B' and resid 110 through 112'
    Processing helix  chain 'B' and resid 113 through 124
      removed outlier: 4.427A  pdb=" N   LYS B 124 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
      removed outlier: 3.584A  pdb=" N   GLN B 137 " --> pdb=" O   PHE B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 149
      removed outlier: 4.208A  pdb=" N   ARG B 145 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 182
    Processing helix  chain 'B' and resid 183 through 186
    Processing helix  chain 'B' and resid 199 through 203
      removed outlier: 3.530A  pdb=" N   ARG B 202 " --> pdb=" O   LEU B 199 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ARG B 203 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 199 through 203'
    Processing helix  chain 'C' and resid 56 through 70
      removed outlier: 3.740A  pdb=" N   ALA C  63 " --> pdb=" O   ALA C  59 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LEU C  64 " --> pdb=" O   PHE C  60 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLN C  65 " --> pdb=" O   HIS C  61 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   LYS C  70 " --> pdb=" O   ASP C  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 70 through 83
      removed outlier: 4.048A  pdb=" N   ILE C  81 " --> pdb=" O   THR C  77 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ILE C  83 " --> pdb=" O   MET C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 102
      removed outlier: 4.045A  pdb=" N   SER C  89 " --> pdb=" O   LEU C  85 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   VAL C  98 " --> pdb=" O   VAL C  94 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN C 100 " --> pdb=" O   LYS C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 134
      removed outlier: 3.594A  pdb=" N   VAL C 127 " --> pdb=" O   ALA C 123 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ALA C 133 " --> pdb=" O   ALA C 129 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   GLU C 134 " --> pdb=" O   GLN C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 160
      removed outlier: 3.815A  pdb=" N   ARG C 153 " --> pdb=" O   LEU C 149 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   ASN C 154 " --> pdb=" O   GLY C 150 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   TRP C 155 " --> pdb=" O   GLU C 151 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   SER C 156 " --> pdb=" O   PHE C 152 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY C 157 " --> pdb=" O   ARG C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 198
      removed outlier: 4.117A  pdb=" N   ASN C 189 " --> pdb=" O   THR C 185 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   THR C 190 " --> pdb=" O   GLU C 186 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU C 191 " --> pdb=" O   SER C 187 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ARG C 194 " --> pdb=" O   THR C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 215
    Processing helix  chain 'C' and resid 216 through 250
      removed outlier: 3.703A  pdb=" N   LEU C 220 " --> pdb=" O   ALA C 216 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ILE C 240 " --> pdb=" O   VAL C 236 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   GLY C 241 " --> pdb=" O   PHE C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 261
      removed outlier: 3.993A  pdb=" N   ASN C 256 " --> pdb=" O   ARG C 252 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 264 through 304
      removed outlier: 3.533A  pdb=" N   ILE C 268 " --> pdb=" O   THR C 264 " (cutoff:3.500A)
      Proline residue:  C 271  - end of helix
      removed outlier: 3.627A  pdb=" N   ILE C 293 " --> pdb=" O   ILE C 289 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU C 294 " --> pdb=" O   LEU C 290 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   GLU C 304 " --> pdb=" O   SER C 300 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 305 through 309
    Processing helix  chain 'C' and resid 319 through 347
      removed outlier: 3.611A  pdb=" N   LEU C 324 " --> pdb=" O   PHE C 320 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   LEU C 325 " --> pdb=" O   ASP C 321 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLN C 344 " --> pdb=" O   LEU C 340 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   HIS C 345 " --> pdb=" O   ALA C 341 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ARG C 347 " --> pdb=" O   VAL C 343 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 348 through 350
      No H-bonds generated for 'chain 'C' and resid 348 through 350'
    Processing helix  chain 'D' and resid 42 through 47
    Processing helix  chain 'D' and resid 73 through 78
      removed outlier: 3.639A  pdb=" N   ARG D  78 " --> pdb=" O   VAL D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 95 through 100
    Processing helix  chain 'D' and resid 101 through 108
      removed outlier: 3.616A  pdb=" N   ILE D 105 " --> pdb=" O   ALA D 101 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ILE D 106 " --> pdb=" O   ILE D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 126
      removed outlier: 4.362A  pdb=" N   ARG D 115 " --> pdb=" O   GLY D 111 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ARG D 116 " --> pdb=" O   ASP D 112 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LYS D 124 " --> pdb=" O   ALA D 120 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL D 125 " --> pdb=" O   ALA D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 153
      removed outlier: 4.067A  pdb=" N   ALA D 151 " --> pdb=" O   GLY D 147 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   VAL D 152 " --> pdb=" O   ILE D 148 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   VAL D 153 " --> pdb=" O   ALA D 149 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 169 through 182
      removed outlier: 3.721A  pdb=" N   GLU D 174 " --> pdb=" O   ASP D 170 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   GLY D 175 " --> pdb=" O   ALA D 171 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   PHE D 180 " --> pdb=" O   ILE D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 183 through 186
    Processing helix  chain 'D' and resid 197 through 202
    Processing helix  chain 'A' and resid 56 through 68
    Processing helix  chain 'A' and resid 70 through 85
      removed outlier: 3.725A  pdb=" N   SER A  84 " --> pdb=" O   VAL A  80 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU A  85 " --> pdb=" O   ILE A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 101
      removed outlier: 3.684A  pdb=" N   SER A  89 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A  98 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ASN A  99 " --> pdb=" O   TYR A  95 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   GLN A 100 " --> pdb=" O   LYS A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 133
      removed outlier: 3.784A  pdb=" N   ALA A 123 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   ALA A 125 " --> pdb=" O   ASP A 121 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   GLY A 126 " --> pdb=" O   ASP A 122 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ALA A 129 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   GLN A 130 " --> pdb=" O   GLY A 126 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU A 131 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 154
    Processing helix  chain 'A' and resid 184 through 192
      removed outlier: 3.653A  pdb=" N   LEU A 188 " --> pdb=" O   GLY A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 250
      removed outlier: 3.550A  pdb=" N   GLY A 219 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 261
      removed outlier: 3.993A  pdb=" N   GLN A 258 " --> pdb=" O   SER A 254 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LYS A 259 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 288
      removed outlier: 3.646A  pdb=" N   ILE A 268 " --> pdb=" O   THR A 264 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU A 269 " --> pdb=" O   ASP A 265 " (cutoff:3.500A)
      Proline residue:  A 271  - end of helix
      removed outlier: 3.696A  pdb=" N   GLY A 275 " --> pdb=" O   PRO A 271 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LEU A 285 " --> pdb=" O   PHE A 281 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LEU A 286 " --> pdb=" O   SER A 282 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   SER A 287 " --> pdb=" O   GLY A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 299
    Processing helix  chain 'A' and resid 299 through 307
      removed outlier: 4.100A  pdb=" N   ALA A 303 " --> pdb=" O   SER A 299 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   GLU A 304 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 310
      No H-bonds generated for 'chain 'A' and resid 308 through 310'
    Processing helix  chain 'A' and resid 319 through 348
      removed outlier: 3.638A  pdb=" N   LEU A 324 " --> pdb=" O   PHE A 320 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LEU A 325 " --> pdb=" O   ASP A 321 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ILE A 333 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   GLY A 334 " --> pdb=" O   CYS A 330 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA A 338 " --> pdb=" O   GLY A 334 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   TRP A 339 " --> pdb=" O   TRP A 335 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL A 343 " --> pdb=" O   TRP A 339 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   HIS A 348 " --> pdb=" O   GLN A 344 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 3
    Processing sheet with id=AA2, first strand: chain 'B' and resid 30 through 32
      removed outlier: 3.737A  pdb=" N   LEU B 191 " --> pdb=" O   LEU B 159 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 173 through 174
      removed outlier: 4.134A  pdb=" N   VAL C 113 " --> pdb=" O   ALA C 174 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLU C 203 " --> pdb=" O   TYR C 114 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 3
    Processing sheet with id=AA5, first strand: chain 'D' and resid 32 through 33
      removed outlier: 3.570A  pdb=" N   GLY D  82 " --> pdb=" O   VAL D 158 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU D 160 " --> pdb=" O   GLY D  82 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 60 through 61

    338 hydrogen bonds defined for protein.
    984 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: 0.98

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.36: 2599
        1.36 -     1.51: 2092
        1.51 -     1.66: 3143
        1.66 -     1.80: 34
        1.80 -     1.95: 24
  Bond restraints: 7892
  Sorted by residual:
  bond pdb=" CA  VAL B  74 "
       pdb=" CB  VAL B  74 "
    ideal  model  delta    sigma   weight residual
    1.534  1.551 -0.016 6.80e-03 2.16e+04 5.89e+00
  bond pdb=" CA  VAL B  74 "
       pdb=" C   VAL B  74 "
    ideal  model  delta    sigma   weight residual
    1.520  1.539 -0.019 8.80e-03 1.29e+04 4.72e+00
  bond pdb=" CA  ASN D 154 "
       pdb=" C   ASN D 154 "
    ideal  model  delta    sigma   weight residual
    1.526  1.556 -0.030 1.75e-02 3.27e+03 2.95e+00
  bond pdb=" C   TYR A 106 "
       pdb=" N   PRO A 107 "
    ideal  model  delta    sigma   weight residual
    1.334  1.373 -0.039 2.34e-02 1.83e+03 2.80e+00
  bond pdb=" CB  ASN D 154 "
       pdb=" CG  ASN D 154 "
    ideal  model  delta    sigma   weight residual
    1.516  1.557 -0.041 2.50e-02 1.60e+03 2.73e+00
  ... (remaining 7887 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.80: 10402
        2.80 -     5.60: 262
        5.60 -     8.40: 44
        8.40 -    11.20: 19
       11.20 -    14.00: 3
  Bond angle restraints: 10730
  Sorted by residual:
  angle pdb=" CB  LYS D 155 "
        pdb=" CG  LYS D 155 "
        pdb=" CD  LYS D 155 "
      ideal   model   delta    sigma   weight residual
     111.30  123.84  -12.54 2.30e+00 1.89e-01 2.97e+01
  angle pdb=" C   ASN A 199 "
        pdb=" CA  ASN A 199 "
        pdb=" CB  ASN A 199 "
      ideal   model   delta    sigma   weight residual
     117.23  110.57    6.66 1.36e+00 5.41e-01 2.40e+01
  angle pdb=" CB  MET D  92 "
        pdb=" CG  MET D  92 "
        pdb=" SD  MET D  92 "
      ideal   model   delta    sigma   weight residual
     112.70  126.70  -14.00 3.00e+00 1.11e-01 2.18e+01
  angle pdb=" C   PRO D 164 "
        pdb=" N   THR D 165 "
        pdb=" CA  THR D 165 "
      ideal   model   delta    sigma   weight residual
     121.54  129.65   -8.11 1.91e+00 2.74e-01 1.80e+01
  angle pdb=" CA  VAL B  74 "
        pdb=" C   VAL B  74 "
        pdb=" N   PRO B  75 "
      ideal   model   delta    sigma   weight residual
     121.00  124.52   -3.52 8.30e-01 1.45e+00 1.79e+01
  ... (remaining 10725 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.85: 4180
       16.85 -    33.70: 385
       33.70 -    50.55: 87
       50.55 -    67.41: 10
       67.41 -    84.26: 5
  Dihedral angle restraints: 4667
    sinusoidal: 1766
      harmonic: 2901
  Sorted by residual:
  dihedral pdb=" CA  VAL D  74 "
           pdb=" C   VAL D  74 "
           pdb=" N   PRO D  75 "
           pdb=" CA  PRO D  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.95   27.05     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  GLU D 163 "
           pdb=" C   GLU D 163 "
           pdb=" N   PRO D 164 "
           pdb=" CA  PRO D 164 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.53   24.47     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" CA  LEU A 260 "
           pdb=" C   LEU A 260 "
           pdb=" N   ILE A 261 "
           pdb=" CA  ILE A 261 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.91   20.09     0      5.00e+00 4.00e-02 1.61e+01
  ... (remaining 4664 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1034
       0.069 -    0.137: 208
       0.137 -    0.206: 24
       0.206 -    0.274: 4
       0.274 -    0.343: 3
  Chirality restraints: 1273
  Sorted by residual:
  chirality pdb=" CB  VAL C 302 "
            pdb=" CA  VAL C 302 "
            pdb=" CG1 VAL C 302 "
            pdb=" CG2 VAL C 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.34 2.00e-01 2.50e+01 2.94e+00
  chirality pdb=" CB  VAL D  74 "
            pdb=" CA  VAL D  74 "
            pdb=" CG1 VAL D  74 "
            pdb=" CG2 VAL D  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.51e+00
  chirality pdb=" CB  ILE D  59 "
            pdb=" CA  ILE D  59 "
            pdb=" CG1 ILE D  59 "
            pdb=" CG2 ILE D  59 "
    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 1270 not shown)

  Planarity restraints: 1363
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D  74 "    0.072 5.00e-02 4.00e+02   1.07e-01 1.83e+01
        pdb=" N   PRO D  75 "   -0.185 5.00e-02 4.00e+02
        pdb=" CA  PRO D  75 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO D  75 "    0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 335 "   -0.019 2.00e-02 2.50e+03   2.05e-02 1.05e+01
        pdb=" CG  TRP C 335 "    0.054 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 335 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 335 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 335 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 335 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 335 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 335 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 335 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 335 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  76 "    0.017 2.00e-02 2.50e+03   2.00e-02 7.00e+00
        pdb=" CG  PHE D  76 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  76 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  76 "    0.014 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  76 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  76 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  76 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1360 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2340
        2.83 -     3.34: 7406
        3.34 -     3.86: 12699
        3.86 -     4.38: 13892
        4.38 -     4.90: 23306
  Nonbonded interactions: 59643
  Sorted by model distance:
  nonbonded pdb=" O   ASP D 169 "
            pdb=" OG  SER D 173 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   GLN C  65 "
            pdb=" OG  SER C  69 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   THR C  86 "
            pdb=" OG  SER C  89 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OE2 GLU B 181 "
            pdb=" OH  TYR B 205 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" OG  SER B 110 "
            pdb=" OD1 ASP B 113 "
     model   vdw
     2.345 3.040
  ... (remaining 59638 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 'A' and (resid 53 through 67 or (resid 68 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 69 through 78 or (resid 79 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 80 through 138 or (resid 139 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 140 through 154 o \ 
r (resid 155 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 
56 through 160 or resid 168 through 185 or (resid 186 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 187 through 317 or (resid 318 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 319 through 351))
  selection = (chain 'C' and (resid 53 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 69 or (resid 70 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 71 through 95 or (resid 96 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 97 through 121 or ( \ 
resid 122 through 125 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 126 through 146 or (resid 147 through 148 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 149 through 179 or (resid 180 through 182 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 183 through 184  \ 
or (resid 185 through 186 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 187 through 193 or (resid 194 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 195 through 204 or (resid 205 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 206 through 296 or (resid 297 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 298 through 311 or ( \ 
resid 312 and (name N or name CA or name C or name O or name CB )) or resid 313  \ 
or (resid 314 and (name N or name CA or name C or name O or name CB )) or resid  \ 
315 through 347 or (resid 348 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 349 through 351))
}
ncs_group {
  reference = (chain 'B' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 13 through 67 or (resid 68 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 69 or (resid 70 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 71 through 92 or (resid 93 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 94 through 301))
  selection = (chain 'D' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 4 through 25 or (resid 26 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 27 through 28 or (resid 29 through 3 \ 
1 and (name N or name CA or name C or name O or name CB )) or resid 32 through 7 \ 
2 or (resid 73 and (name N or name CA or name C or name O or name CB )) or resid \ 
 74 through 78 or (resid 79 and (name N or name CA or name C or name O or name C \ 
B )) or resid 80 through 131 or (resid 132 and (name N or name CA or name C or n \ 
ame O or name CB )) or resid 133 through 154 or (resid 155 and (name N or name C \ 
A or name C or name O or name CB )) or resid 156 through 184 or (resid 185 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 186 through 217 or  \ 
resid 301))
}

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:             1.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.120
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
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      :  0.004   0.054   7892  Z= 0.207
  Angle     :  1.097  14.000  10730  Z= 0.528
  Chirality :  0.056   0.343   1273
  Planarity :  0.007   0.107   1363
  Dihedral  : 13.870  84.257   2803
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.05 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.63 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.33 (0.23), residues: 1009
  helix: -2.01 (0.19), residues: 501
  sheet: -1.63 (0.63), residues: 70
  loop : -2.44 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG C 252 
 TYR   0.030   0.002   TYR C 106 
 PHE   0.046   0.002   PHE D  76 
 TRP   0.054   0.002   TRP C 335 
 HIS   0.010   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 7892)
  covalent geometry    : angle       1.09668 (10730)
  hydrogen bonds       : bond        0.19637 (  338)
  hydrogen bonds       : angle       6.55509 (  984)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 200
  time to evaluate  : 0.284 
Fit side-chains
REVERT: B   87 ASP cc_start: 0.8316 (p0) cc_final: 0.8059 (p0)
REVERT: B  116 ARG cc_start: 0.8828 (ptt90) cc_final: 0.8567 (tmm-80)
REVERT: C   61 HIS cc_start: 0.8298 (t-90) cc_final: 0.8002 (t70)
REVERT: D   59 ILE cc_start: 0.5845 (tp) cc_final: 0.5644 (tp)
REVERT: D   85 PHE cc_start: 0.8401 (m-10) cc_final: 0.8069 (m-10)
REVERT: D   87 ASP cc_start: 0.8192 (p0) cc_final: 0.7866 (p0)
REVERT: D   89 HIS cc_start: 0.6507 (m90) cc_final: 0.6193 (m90)
REVERT: A   95 TYR cc_start: 0.7979 (t80) cc_final: 0.7714 (t80)
REVERT: A  100 GLN cc_start: 0.9245 (mp10) cc_final: 0.9028 (mp10)
REVERT: A  206 MET cc_start: 0.4213 (mmp) cc_final: 0.3592 (mmp)
REVERT: A  232 MET cc_start: 0.8157 (mmm) cc_final: 0.7573 (mtt)
REVERT: A  344 GLN cc_start: 0.7785 (tt0) cc_final: 0.7154 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 200
  average time/residue: 0.0766
  time to fit residues: 21.0593
Evaluate side-chains
  163 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0170
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    8.9990
   overall best weight:    0.7220

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

Flipped N/Q/H residues before XYZ refinement:
** B  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 143 GLN
B 144 GLN
D 154 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.119413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.090986 restraints weight = 23743.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.093279 restraints weight = 13884.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.094784 restraints weight = 9344.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.095706 restraints weight = 7015.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.096632 restraints weight = 5717.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7892  Z= 0.125
  Angle     :  0.666   7.093  10730  Z= 0.328
  Chirality :  0.042   0.191   1273
  Planarity :  0.005   0.058   1363
  Dihedral  :  7.903  59.536   1130
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  4.46 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.84 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.16 (0.25), residues: 1009
  helix: -0.76 (0.22), residues: 521
  sheet: -1.39 (0.70), residues: 62
  loop : -2.24 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 203 
 TYR   0.014   0.001   TYR B  11 
 PHE   0.019   0.001   PHE A 249 
 TRP   0.026   0.001   TRP C 335 
 HIS   0.004   0.001   HIS A 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 7892)
  covalent geometry    : angle       0.66628 (10730)
  hydrogen bonds       : bond        0.03956 (  338)
  hydrogen bonds       : angle       4.55922 (  984)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 173
  time to evaluate  : 0.299 
Fit side-chains
REVERT: B  116 ARG cc_start: 0.8804 (ptt90) cc_final: 0.8520 (tmm-80)
REVERT: C   61 HIS cc_start: 0.8343 (t-90) cc_final: 0.8024 (t70)
REVERT: D   87 ASP cc_start: 0.8232 (p0) cc_final: 0.7867 (p0)
REVERT: D   89 HIS cc_start: 0.6745 (m90) cc_final: 0.6022 (m90)
REVERT: D  189 THR cc_start: 0.8343 (m) cc_final: 0.8116 (p)
REVERT: A   95 TYR cc_start: 0.7914 (t80) cc_final: 0.7702 (t80)
REVERT: A  100 GLN cc_start: 0.9130 (mp10) cc_final: 0.8894 (mp10)
REVERT: A  206 MET cc_start: 0.4121 (mmp) cc_final: 0.3222 (mmp)
REVERT: A  344 GLN cc_start: 0.7748 (tt0) cc_final: 0.7195 (tm-30)
  outliers start: 17
  outliers final: 11
  residues processed: 177
  average time/residue: 0.0608
  time to fit residues: 15.3777
Evaluate side-chains
  168 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 157
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain C residue  122 ASP
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  348 HIS
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  296 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 77 optimal weight:    0.0970
   chunk 2 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 6 optimal weight:    0.1980
   chunk 54 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:   20.0000
   chunk 39 optimal weight:    4.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
B 216 HIS
D 154 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.117675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.089302 restraints weight = 23573.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.091495 restraints weight = 13835.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.093059 restraints weight = 9388.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.094026 restraints weight = 6991.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.094739 restraints weight = 5684.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7892  Z= 0.124
  Angle     :  0.624   8.240  10730  Z= 0.309
  Chirality :  0.040   0.178   1273
  Planarity :  0.004   0.058   1363
  Dihedral  :  7.665  59.783   1130
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  4.76 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.87 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.45 (0.26), residues: 1009
  helix: -0.04 (0.23), residues: 518
  sheet: -1.64 (0.73), residues: 55
  loop : -2.00 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 252 
 TYR   0.012   0.001   TYR B  11 
 PHE   0.012   0.001   PHE B 180 
 TRP   0.021   0.001   TRP C 335 
 HIS   0.004   0.001   HIS B  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7892)
  covalent geometry    : angle       0.62387 (10730)
  hydrogen bonds       : bond        0.03277 (  338)
  hydrogen bonds       : angle       4.03060 (  984)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 169
  time to evaluate  : 0.365 
Fit side-chains
REVERT: B   83 MET cc_start: 0.7601 (mmm) cc_final: 0.7363 (tpt)
REVERT: B  116 ARG cc_start: 0.8811 (ptt90) cc_final: 0.8489 (tmm-80)
REVERT: C   61 HIS cc_start: 0.8426 (t-90) cc_final: 0.8138 (t70)
REVERT: C  232 MET cc_start: 0.8539 (mmp) cc_final: 0.8095 (mmp)
REVERT: C  347 ARG cc_start: 0.8269 (mmp80) cc_final: 0.7968 (mmm160)
REVERT: D  189 THR cc_start: 0.8508 (m) cc_final: 0.8259 (p)
REVERT: A  100 GLN cc_start: 0.9159 (mp10) cc_final: 0.8754 (mp10)
REVERT: A  206 MET cc_start: 0.4346 (mmp) cc_final: 0.3477 (mmp)
REVERT: A  344 GLN cc_start: 0.7745 (tt0) cc_final: 0.7273 (tm-30)
  outliers start: 19
  outliers final: 14
  residues processed: 175
  average time/residue: 0.0714
  time to fit residues: 17.5527
Evaluate side-chains
  166 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain C residue  122 ASP
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  348 HIS
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue  170 ASP
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  296 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    8.9990
   chunk 51 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0770
   chunk 41 optimal weight:    0.9990
   chunk 94 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 80 optimal weight:    8.9990
   chunk 86 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0370
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.6220

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

Flipped N/Q/H residues before XYZ refinement:
B  24 HIS
B  89 HIS
B 143 GLN
** C  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 256 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.117876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.089461 restraints weight = 23996.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.091753 restraints weight = 13867.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.093273 restraints weight = 9262.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.094200 restraints weight = 6878.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.094979 restraints weight = 5589.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7892  Z= 0.109
  Angle     :  0.610   7.107  10730  Z= 0.297
  Chirality :  0.040   0.175   1273
  Planarity :  0.003   0.057   1363
  Dihedral  :  7.341  53.044   1130
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  4.56 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 22.26 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.27), residues: 1009
  helix:  0.32 (0.23), residues: 526
  sheet: -1.24 (0.69), residues: 69
  loop : -1.99 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 252 
 TYR   0.015   0.001   TYR A  95 
 PHE   0.021   0.001   PHE D  76 
 TRP   0.016   0.001   TRP C 335 
 HIS   0.007   0.001   HIS B  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7892)
  covalent geometry    : angle       0.61013 (10730)
  hydrogen bonds       : bond        0.03038 (  338)
  hydrogen bonds       : angle       3.88103 (  984)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.208 
Fit side-chains
REVERT: B  116 ARG cc_start: 0.8812 (ptt90) cc_final: 0.8482 (tmm-80)
REVERT: C   61 HIS cc_start: 0.8376 (t-90) cc_final: 0.8031 (t-90)
REVERT: C  232 MET cc_start: 0.8441 (mmp) cc_final: 0.8098 (mmp)
REVERT: C  347 ARG cc_start: 0.8286 (mmp80) cc_final: 0.8073 (mmm160)
REVERT: D  189 THR cc_start: 0.8505 (m) cc_final: 0.8258 (p)
REVERT: A  100 GLN cc_start: 0.9154 (mp10) cc_final: 0.8890 (mp10)
REVERT: A  206 MET cc_start: 0.4345 (mmp) cc_final: 0.3449 (mmp)
  outliers start: 24
  outliers final: 17
  residues processed: 173
  average time/residue: 0.0650
  time to fit residues: 16.1159
Evaluate side-chains
  174 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  214 HIS
Chi-restraints excluded: chain C residue  122 ASP
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain C residue  348 HIS
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  296 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 77 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B  89 HIS
B 143 GLN
C  65 GLN
D  19 GLN
D 154 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.117343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.089082 restraints weight = 23962.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.091352 restraints weight = 13800.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.092835 restraints weight = 9220.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.093974 restraints weight = 6784.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.094514 restraints weight = 5445.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7892  Z= 0.117
  Angle     :  0.630   8.464  10730  Z= 0.305
  Chirality :  0.041   0.175   1273
  Planarity :  0.003   0.057   1363
  Dihedral  :  7.084  54.500   1130
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  4.36 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 22.89 %
    Favored  : 73.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.27), residues: 1009
  helix:  0.51 (0.23), residues: 527
  sheet: -1.54 (0.66), residues: 74
  loop : -1.92 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 252 
 TYR   0.013   0.001   TYR A  95 
 PHE   0.019   0.001   PHE D  76 
 TRP   0.015   0.001   TRP C 335 
 HIS   0.003   0.001   HIS C 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7892)
  covalent geometry    : angle       0.62957 (10730)
  hydrogen bonds       : bond        0.02960 (  338)
  hydrogen bonds       : angle       3.78367 (  984)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 164
  time to evaluate  : 0.298 
Fit side-chains
REVERT: B  116 ARG cc_start: 0.8804 (ptt90) cc_final: 0.8471 (tmm-80)
REVERT: C   61 HIS cc_start: 0.8390 (t-90) cc_final: 0.8166 (t70)
REVERT: C  347 ARG cc_start: 0.8298 (mmp80) cc_final: 0.8056 (mmm160)
REVERT: D  182 GLU cc_start: 0.8630 (pp20) cc_final: 0.8075 (pp20)
REVERT: D  189 THR cc_start: 0.8534 (m) cc_final: 0.8299 (p)
REVERT: A  100 GLN cc_start: 0.9195 (mp10) cc_final: 0.8920 (mp10)
REVERT: A  206 MET cc_start: 0.4310 (mmp) cc_final: 0.3739 (mmp)
  outliers start: 29
  outliers final: 19
  residues processed: 176
  average time/residue: 0.0594
  time to fit residues: 15.0782
Evaluate side-chains
  173 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 154
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  148 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain C residue  122 ASP
Chi-restraints excluded: chain C residue  253 ASP
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain C residue  348 HIS
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  296 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 81 optimal weight:   30.0000
   chunk 21 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** D  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 216 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.110545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.081561 restraints weight = 25107.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.083530 restraints weight = 14647.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.084824 restraints weight = 9974.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.085793 restraints weight = 7587.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.086267 restraints weight = 6202.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063   7892  Z= 0.265
  Angle     :  0.738   9.153  10730  Z= 0.372
  Chirality :  0.044   0.186   1273
  Planarity :  0.004   0.059   1363
  Dihedral  :  7.266  52.939   1130
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.86 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 23.14 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.00 (0.27), residues: 1009
  helix:  0.39 (0.23), residues: 540
  sheet: -1.55 (0.66), residues: 71
  loop : -1.95 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 245 
 TYR   0.016   0.002   TYR A  95 
 PHE   0.024   0.002   PHE D 183 
 TRP   0.019   0.002   TRP C 335 
 HIS   0.005   0.001   HIS D  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00584 ( 7892)
  covalent geometry    : angle       0.73819 (10730)
  hydrogen bonds       : bond        0.03455 (  338)
  hydrogen bonds       : angle       4.09343 (  984)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 160
  time to evaluate  : 0.229 
Fit side-chains
REVERT: B  189 THR cc_start: 0.8701 (m) cc_final: 0.8447 (p)
REVERT: C   61 HIS cc_start: 0.8446 (t-90) cc_final: 0.8230 (t70)
REVERT: C  232 MET cc_start: 0.8646 (mmp) cc_final: 0.8373 (mmm)
REVERT: C  347 ARG cc_start: 0.8435 (mmp80) cc_final: 0.8211 (mmm160)
REVERT: A  100 GLN cc_start: 0.9329 (mp10) cc_final: 0.8984 (mp10)
REVERT: A  206 MET cc_start: 0.5017 (mmp) cc_final: 0.4772 (mmt)
  outliers start: 35
  outliers final: 27
  residues processed: 178
  average time/residue: 0.0661
  time to fit residues: 16.2039
Evaluate side-chains
  172 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain C residue  253 ASP
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  312 LYS
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  348 HIS
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue  170 ASP
Chi-restraints excluded: chain D residue  191 LEU
Chi-restraints excluded: chain D residue  216 HIS
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  296 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:   30.0000
   chunk 63 optimal weight:    0.9990
   chunk 85 optimal weight:    0.5980
   chunk 82 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0040
   chunk 20 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 92 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
** B  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  89 HIS
B  99 ASN
D  19 GLN
** D  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 154 ASN
A 258 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.113327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.083798 restraints weight = 24533.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.085975 restraints weight = 14117.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.087459 restraints weight = 9492.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.088346 restraints weight = 7117.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.089032 restraints weight = 5841.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7892  Z= 0.128
  Angle     :  0.696  12.275  10730  Z= 0.331
  Chirality :  0.042   0.165   1273
  Planarity :  0.004   0.063   1363
  Dihedral  :  7.090  57.458   1130
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.15 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 22.77 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.27), residues: 1009
  helix:  0.57 (0.23), residues: 533
  sheet: -1.41 (0.68), residues: 71
  loop : -1.88 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 252 
 TYR   0.016   0.001   TYR A  95 
 PHE   0.014   0.001   PHE C 281 
 TRP   0.014   0.001   TRP C 335 
 HIS   0.016   0.002   HIS D 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7892)
  covalent geometry    : angle       0.69600 (10730)
  hydrogen bonds       : bond        0.03147 (  338)
  hydrogen bonds       : angle       3.86030 (  984)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 168
  time to evaluate  : 0.298 
Fit side-chains
REVERT: B  163 GLU cc_start: 0.8754 (tt0) cc_final: 0.8476 (tt0)
REVERT: B  189 THR cc_start: 0.8744 (m) cc_final: 0.8533 (p)
REVERT: C   61 HIS cc_start: 0.8433 (t-90) cc_final: 0.8187 (t70)
REVERT: C  232 MET cc_start: 0.8561 (mmp) cc_final: 0.8269 (mmm)
REVERT: C  347 ARG cc_start: 0.8282 (mmp80) cc_final: 0.7935 (mmm160)
REVERT: D   25 MET cc_start: 0.8623 (tpt) cc_final: 0.8199 (tpt)
REVERT: A  100 GLN cc_start: 0.9250 (mp10) cc_final: 0.8927 (mp10)
REVERT: A  206 MET cc_start: 0.5155 (mmp) cc_final: 0.4912 (mmt)
  outliers start: 36
  outliers final: 24
  residues processed: 186
  average time/residue: 0.0753
  time to fit residues: 19.8464
Evaluate side-chains
  177 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 153
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain C residue  122 ASP
Chi-restraints excluded: chain C residue  253 ASP
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain C residue  348 HIS
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  191 LEU
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  258 GLN
Chi-restraints excluded: chain A residue  296 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 53 optimal weight:    8.9990
   chunk 49 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 27 optimal weight:   20.0000
   chunk 94 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B  71 ASN
B  89 HIS
** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 143 GLN
** D  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 154 ASN
D 216 HIS
A 258 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.112174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.083062 restraints weight = 24758.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.085154 restraints weight = 14457.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.086576 restraints weight = 9793.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.087538 restraints weight = 7376.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.088125 restraints weight = 6036.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.3069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7892  Z= 0.162
  Angle     :  0.716  11.358  10730  Z= 0.344
  Chirality :  0.044   0.328   1273
  Planarity :  0.004   0.056   1363
  Dihedral  :  7.028  57.655   1130
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.05 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 23.40 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.79 (0.27), residues: 1009
  helix:  0.62 (0.23), residues: 537
  sheet: -1.51 (0.68), residues: 71
  loop : -1.92 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  78 
 TYR   0.015   0.001   TYR A  95 
 PHE   0.014   0.001   PHE B   4 
 TRP   0.015   0.001   TRP C 335 
 HIS   0.006   0.001   HIS D 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 7892)
  covalent geometry    : angle       0.71575 (10730)
  hydrogen bonds       : bond        0.03175 (  338)
  hydrogen bonds       : angle       3.87882 (  984)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 156
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: B  163 GLU cc_start: 0.8775 (tt0) cc_final: 0.8465 (tt0)
REVERT: B  189 THR cc_start: 0.8771 (m) cc_final: 0.8532 (p)
REVERT: C   61 HIS cc_start: 0.8432 (t-90) cc_final: 0.8194 (t70)
REVERT: C  232 MET cc_start: 0.8546 (mmp) cc_final: 0.8224 (mmm)
REVERT: C  347 ARG cc_start: 0.8252 (mmp80) cc_final: 0.7902 (ttp-170)
REVERT: D  142 GLU cc_start: 0.8691 (pm20) cc_final: 0.8393 (pm20)
REVERT: D  160 LEU cc_start: 0.9177 (mt) cc_final: 0.8881 (mt)
REVERT: A  100 GLN cc_start: 0.9292 (mp10) cc_final: 0.8975 (mp10)
REVERT: A  206 MET cc_start: 0.5075 (mmp) cc_final: 0.4781 (mmt)
REVERT: A  232 MET cc_start: 0.7942 (mmm) cc_final: 0.7565 (mtt)
  outliers start: 34
  outliers final: 26
  residues processed: 174
  average time/residue: 0.0697
  time to fit residues: 17.1002
Evaluate side-chains
  174 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  253 ASP
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain C residue  348 HIS
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  191 LEU
Chi-restraints excluded: chain D residue  216 HIS
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  336 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 28 optimal weight:   40.0000
   chunk 20 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0070
   chunk 82 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.3804

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

Flipped N/Q/H residues before XYZ refinement:
B  89 HIS
** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 143 GLN
** D  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 154 ASN
D 214 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.112034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.083092 restraints weight = 24868.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.085176 restraints weight = 14440.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.086480 restraints weight = 9713.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.087539 restraints weight = 7362.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.088176 restraints weight = 5981.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7892  Z= 0.156
  Angle     :  0.723  11.850  10730  Z= 0.344
  Chirality :  0.044   0.302   1273
  Planarity :  0.004   0.055   1363
  Dihedral  :  7.030  59.480   1130
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.65 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 23.90 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.27), residues: 1009
  helix:  0.72 (0.23), residues: 530
  sheet: -1.51 (0.68), residues: 71
  loop : -1.86 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  78 
 TYR   0.015   0.001   TYR A  95 
 PHE   0.016   0.001   PHE B 180 
 TRP   0.015   0.001   TRP C 335 
 HIS   0.011   0.001   HIS D 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 7892)
  covalent geometry    : angle       0.72319 (10730)
  hydrogen bonds       : bond        0.03139 (  338)
  hydrogen bonds       : angle       3.86896 (  984)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 156
  time to evaluate  : 0.252 
Fit side-chains
REVERT: B  163 GLU cc_start: 0.8764 (tt0) cc_final: 0.8450 (tt0)
REVERT: B  189 THR cc_start: 0.8735 (m) cc_final: 0.8502 (p)
REVERT: C   61 HIS cc_start: 0.8408 (t-90) cc_final: 0.8146 (t70)
REVERT: C  232 MET cc_start: 0.8588 (mmp) cc_final: 0.8249 (mmm)
REVERT: C  347 ARG cc_start: 0.8243 (mmp80) cc_final: 0.7924 (ttp-170)
REVERT: D  160 LEU cc_start: 0.9183 (mt) cc_final: 0.8888 (mt)
REVERT: A  100 GLN cc_start: 0.9284 (mp10) cc_final: 0.8951 (mp10)
REVERT: A  206 MET cc_start: 0.5127 (mmp) cc_final: 0.4810 (mmt)
REVERT: A  232 MET cc_start: 0.8013 (mmm) cc_final: 0.7678 (mtt)
  outliers start: 30
  outliers final: 25
  residues processed: 171
  average time/residue: 0.0700
  time to fit residues: 16.9736
Evaluate side-chains
  179 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 154
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  253 ASP
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain C residue  348 HIS
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  191 LEU
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  336 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 80 optimal weight:    9.9990
   chunk 76 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 42 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 33 optimal weight:   10.0000
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 143 GLN
D 154 ASN
D 216 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.113490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.084148 restraints weight = 24625.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.086397 restraints weight = 14088.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.087865 restraints weight = 9409.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.088668 restraints weight = 7031.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.089450 restraints weight = 5818.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.3171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7892  Z= 0.131
  Angle     :  0.720  12.282  10730  Z= 0.341
  Chirality :  0.044   0.285   1273
  Planarity :  0.004   0.056   1363
  Dihedral  :  6.905  57.143   1130
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.15 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 24.40 %
    Favored  : 72.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.27), residues: 1009
  helix:  0.74 (0.23), residues: 538
  sheet: -1.44 (0.69), residues: 71
  loop : -1.92 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  78 
 TYR   0.018   0.001   TYR C  58 
 PHE   0.030   0.001   PHE D  76 
 TRP   0.014   0.001   TRP C 335 
 HIS   0.007   0.001   HIS D 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7892)
  covalent geometry    : angle       0.72021 (10730)
  hydrogen bonds       : bond        0.03121 (  338)
  hydrogen bonds       : angle       3.82789 (  984)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 157
  time to evaluate  : 0.226 
Fit side-chains
REVERT: B  162 ASP cc_start: 0.7726 (t0) cc_final: 0.7196 (t0)
REVERT: B  163 GLU cc_start: 0.8735 (tt0) cc_final: 0.8307 (tt0)
REVERT: C   61 HIS cc_start: 0.8420 (t-90) cc_final: 0.8140 (t70)
REVERT: C  232 MET cc_start: 0.8635 (mmp) cc_final: 0.8280 (mmm)
REVERT: C  347 ARG cc_start: 0.8204 (mmp80) cc_final: 0.7890 (ttp-170)
REVERT: D  142 GLU cc_start: 0.8683 (pm20) cc_final: 0.8402 (pm20)
REVERT: A  100 GLN cc_start: 0.9255 (mp10) cc_final: 0.8903 (mp10)
REVERT: A  206 MET cc_start: 0.5312 (mmp) cc_final: 0.5005 (mmt)
REVERT: A  232 MET cc_start: 0.8001 (mmm) cc_final: 0.7773 (mtt)
  outliers start: 27
  outliers final: 22
  residues processed: 170
  average time/residue: 0.0731
  time to fit residues: 17.3478
Evaluate side-chains
  173 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 151
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  253 ASP
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain C residue  348 HIS
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  191 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  336 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 3 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 28 optimal weight:   40.0000
   chunk 24 optimal weight:    0.0970
   overall best weight:    1.4182

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

Flipped N/Q/H residues before XYZ refinement:
B  89 HIS
** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 143 GLN
** D  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 154 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.111604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.082548 restraints weight = 24921.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.084646 restraints weight = 14475.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.086017 restraints weight = 9787.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.087037 restraints weight = 7420.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.087530 restraints weight = 6040.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7892  Z= 0.158
  Angle     :  0.721  11.636  10730  Z= 0.345
  Chirality :  0.044   0.273   1273
  Planarity :  0.004   0.056   1363
  Dihedral  :  6.952  56.871   1130
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.35 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 24.78 %
    Favored  : 71.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.63 (0.27), residues: 1009
  helix:  0.79 (0.23), residues: 537
  sheet: -1.46 (0.69), residues: 71
  loop : -1.90 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 185 
 TYR   0.015   0.002   TYR C  58 
 PHE   0.023   0.001   PHE D  76 
 TRP   0.015   0.001   TRP C 335 
 HIS   0.013   0.001   HIS D 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 7892)
  covalent geometry    : angle       0.72131 (10730)
  hydrogen bonds       : bond        0.03134 (  338)
  hydrogen bonds       : angle       3.89887 (  984)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1270.49 seconds
wall clock time: 22 minutes 39.04 seconds (1359.04 seconds total)