Starting phenix.real_space_refine
on Sun Jul 27 07:55:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hd0_34668/07_2025/8hd0_34668.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hd0_34668/07_2025/8hd0_34668.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hd0_34668/07_2025/8hd0_34668.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hd0_34668/07_2025/8hd0_34668.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hd0_34668/07_2025/8hd0_34668.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hd0_34668/07_2025/8hd0_34668.cif"
  }
  resolution = 3.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.012
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      30      5.16       5
     C    5699      2.51       5
     N    1682      2.21       5
     O    1679      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9096
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1669
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 7, 'TRANS': 210}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 1670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1670
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 210}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "C"
      Number of atoms: 1918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 1918
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 108}
          Link IDs: {'PTRANS': 9, 'TRANS': 289}
          Unresolved non-hydrogen bonds: 393
          Unresolved non-hydrogen angles: 505
          Unresolved non-hydrogen dihedrals: 313
          Unresolved non-hydrogen chiralities: 35
          Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 248
    Chain: "D"
      Number of atoms: 1888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 1888
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 117}
          Link IDs: {'PTRANS': 9, 'TRANS': 289}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 425
          Unresolved non-hydrogen angles: 547
          Unresolved non-hydrogen dihedrals: 337
          Unresolved non-hydrogen chiralities: 41
          Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 264
    Chain: "E"
      Number of atoms: 1889
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 380, 1869
          Classifications: {'peptide': 380}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 300}
          Link IDs: {'PTRANS': 8, 'TRANS': 371}
          Unresolved chain link angles: 8
          Unresolved non-hydrogen bonds: 1137
          Unresolved non-hydrogen angles: 1428
          Unresolved non-hydrogen dihedrals: 923
          Unresolved non-hydrogen chiralities: 85
          Planarities with less than four sites: {'GLN:plan1': 49, 'HIS:plan': 3, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 7, 'ARG%COO:plan': 1, 'PHE:plan': 4, 'GLU:plan': 36, 'ARG:plan': 34}
          Unresolved non-hydrogen planarities: 704
      Conformer: "B"
        Number of residues, atoms: 380, 1869
          Classifications: {'peptide': 380}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 300}
          Link IDs: {'PTRANS': 8, 'TRANS': 371}
          Unresolved chain link angles: 8
          Unresolved non-hydrogen bonds: 1137
          Unresolved non-hydrogen angles: 1428
          Unresolved non-hydrogen dihedrals: 923
          Unresolved non-hydrogen chiralities: 85
          Planarities with less than four sites: {'GLN:plan1': 49, 'HIS:plan': 3, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 7, 'ARG%COO:plan': 1, 'PHE:plan': 4, 'GLU:plan': 36, 'ARG:plan': 34}
          Unresolved non-hydrogen planarities: 704
          bond proxies already assigned to first conformer: 1844
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  AGLU E 233 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BGLU E 233 " occ=0.50
    residue:
      pdb=" N  AARG E 237 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BARG E 237 " occ=0.50
    residue:
      pdb=" N  AARG E 262 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BARG E 262 " occ=0.50
    residue:
      pdb=" N  AVAL E 302 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BVAL E 302 " occ=0.50
  Time building chain proxies: 10.99, per 1000 atoms: 1.21
  Number of scatterers: 9096
  At special positions: 0
  Unit cell: (68.04, 91.56, 253.68, 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      30     16.00
     P       6     15.00
     O    1679      8.00
     N    1682      7.00
     C    5699      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.83
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2592

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 9 sheets defined
      58.8% alpha, 8.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 50
    Processing helix  chain 'A' and resid 73 through 80
      removed outlier: 3.608A  pdb=" N   LEU A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 108
      Proline residue:  A 103  - end of helix
    Processing helix  chain 'A' and resid 110 through 125
      removed outlier: 3.857A  pdb=" N   VAL A 125 " --> pdb=" O   ALA A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 131
    Processing helix  chain 'A' and resid 134 through 138
    Processing helix  chain 'A' and resid 139 through 152
    Processing helix  chain 'A' and resid 153 through 155
      No H-bonds generated for 'chain 'A' and resid 153 through 155'
    Processing helix  chain 'A' and resid 169 through 185
    Processing helix  chain 'A' and resid 196 through 201
      removed outlier: 4.217A  pdb=" N   ILE A 200 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 50
    Processing helix  chain 'B' and resid 73 through 77
    Processing helix  chain 'B' and resid 95 through 108
      Proline residue:  B 103  - end of helix
    Processing helix  chain 'B' and resid 110 through 124
    Processing helix  chain 'B' and resid 127 through 131
      removed outlier: 3.505A  pdb=" N   ALA B 131 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
      removed outlier: 3.604A  pdb=" N   LEU B 138 " --> pdb=" O   PRO B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 153
    Processing helix  chain 'B' and resid 169 through 185
    Processing helix  chain 'B' and resid 197 through 202
      removed outlier: 3.586A  pdb=" N   ARG B 202 " --> pdb=" O   ASN B 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 79
    Processing helix  chain 'C' and resid 80 through 107
      removed outlier: 3.635A  pdb=" N   VAL C  90 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   LEU C  97 " --> pdb=" O   ILE C  93 " (cutoff:3.500A)
      Proline residue:  C  98  - end of helix
      removed outlier: 4.186A  pdb=" N   MET C 103 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL C 104 " --> pdb=" O   VAL C 100 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   TYR C 105 " --> pdb=" O   CYS C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 141
      removed outlier: 3.887A  pdb=" N   ALA C 135 " --> pdb=" O   ASP C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 156 through 165
      removed outlier: 3.856A  pdb=" N   GLY C 160 " --> pdb=" O   GLU C 156 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   GLU C 161 " --> pdb=" O   ASP C 157 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   PHE C 162 " --> pdb=" O   ALA C 158 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 189 through 194
      removed outlier: 3.609A  pdb=" N   GLY C 194 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 207
      removed outlier: 3.632A  pdb=" N   THR C 200 " --> pdb=" O   GLU C 196 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   LEU C 201 " --> pdb=" O   SER C 197 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASP C 203 " --> pdb=" O   ASN C 199 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 225
    Processing helix  chain 'C' and resid 229 through 261
      removed outlier: 3.680A  pdb=" N   SER C 235 " --> pdb=" O   VAL C 231 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   ALA C 236 " --> pdb=" O   GLY C 232 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   PHE C 247 " --> pdb=" O   VAL C 243 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ARG C 261 " --> pdb=" O   SER C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 270
      removed outlier: 3.668A  pdb=" N   ILE C 265 " --> pdb=" O   ARG C 261 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 279 through 300
      removed outlier: 3.511A  pdb=" N   GLY C 285 " --> pdb=" O   PRO C 281 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LEU C 289 " --> pdb=" O   GLY C 285 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU C 296 " --> pdb=" O   SER C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 320
      removed outlier: 3.925A  pdb=" N   SER C 310 " --> pdb=" O   LEU C 306 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   ALA C 311 " --> pdb=" O   ARG C 307 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLN C 317 " --> pdb=" O   ALA C 313 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   VAL C 318 " --> pdb=" O   GLU C 314 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 329 through 355
      removed outlier: 4.134A  pdb=" N   LEU C 335 " --> pdb=" O   ASP C 331 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 64 through 79
    Processing helix  chain 'D' and resid 80 through 116
      removed outlier: 4.159A  pdb=" N   LEU D  97 " --> pdb=" O   ILE D  93 " (cutoff:3.500A)
      Proline residue:  D  98  - end of helix
      removed outlier: 3.641A  pdb=" N   TYR D 116 " --> pdb=" O   ALA D 112 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 130 through 141
    Processing helix  chain 'D' and resid 156 through 164
      removed outlier: 3.573A  pdb=" N   GLY D 160 " --> pdb=" O   GLU D 156 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLU D 161 " --> pdb=" O   ASP D 157 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   PHE D 162 " --> pdb=" O   ALA D 158 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 189 through 194
      removed outlier: 3.912A  pdb=" N   GLY D 194 " --> pdb=" O   LEU D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 207
      removed outlier: 5.036A  pdb=" N   THR D 200 " --> pdb=" O   GLU D 196 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   LEU D 201 " --> pdb=" O   SER D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 219 through 261
      removed outlier: 4.306A  pdb=" N   SER D 235 " --> pdb=" O   VAL D 231 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 264 through 271
      removed outlier: 4.333A  pdb=" N   GLN D 268 " --> pdb=" O   SER D 264 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ILE D 271 " --> pdb=" O   VAL D 267 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 274 through 319
      removed outlier: 3.512A  pdb=" N   ARG D 280 " --> pdb=" O   GLY D 276 " (cutoff:3.500A)
      Proline residue:  D 281  - end of helix
      removed outlier: 3.789A  pdb=" N   LEU D 289 " --> pdb=" O   GLY D 285 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   SER D 310 " --> pdb=" O   LEU D 306 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   ALA D 311 " --> pdb=" O   ARG D 307 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   VAL D 312 " --> pdb=" O   LEU D 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 329 through 359
      removed outlier: 3.548A  pdb=" N   ARG D 357 " --> pdb=" O   VAL D 353 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   HIS D 358 " --> pdb=" O   GLN D 354 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 41 through 51
    Processing helix  chain 'E' and resid 52 through 123
      removed outlier: 4.657A  pdb=" N   GLN E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 144 through 150
    Processing helix  chain 'E' and resid 152 through 217
    Processing helix  chain 'E' and resid 221 through 247
    Processing helix  chain 'E' and resid 248 through 271
      removed outlier: 4.129A  pdb=" N   GLU E 252 " --> pdb=" O   LYS E 248 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 278 through 286
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 25
      removed outlier: 5.436A  pdb=" N   GLN A  19 " --> pdb=" O   LYS A   9 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   LYS A   9 " --> pdb=" O   GLN A  19 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   PHE A  23 " --> pdb=" O   GLU A   5 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   GLU A   5 " --> pdb=" O   PHE A  23 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   MET A  25 " --> pdb=" O   ARG A   3 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   ARG A   3 " --> pdb=" O   MET A  25 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   VAL A   7 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ALA A  56 " --> pdb=" O   VAL A   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84
      removed outlier: 6.465A  pdb=" N   LEU A 159 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   ALA A 193 " --> pdb=" O   LEU A 159 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ALA A 161 " --> pdb=" O   ALA A 193 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ALA A  31 " --> pdb=" O   MET A 192 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   PHE A  32 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   LEU A 210 " --> pdb=" O   PHE A  32 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   THR A  34 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 25
      removed outlier: 6.492A  pdb=" N   ALA B  17 " --> pdb=" O   ALA B  10 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   ALA B  10 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   GLN B  19 " --> pdb=" O   SER B   8 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   SER B   8 " --> pdb=" O   GLN B  19 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   VAL B  21 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   VAL B   7 " --> pdb=" O   ALA B  56 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ALA B  56 " --> pdb=" O   VAL B   7 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 84
      removed outlier: 6.401A  pdb=" N   GLY B  82 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   ASP B 162 " --> pdb=" O   GLY B  82 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   ILE B  84 " --> pdb=" O   ASP B 162 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   LEU B 159 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   ALA B 193 " --> pdb=" O   LEU B 159 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ALA B 161 " --> pdb=" O   ALA B 193 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA B  31 " --> pdb=" O   VAL B 190 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 150 through 151
    Processing sheet with id=AA6, first strand: chain 'D' and resid 151 through 152
    Processing sheet with id=AA7, first strand: chain 'E' and resid 313 through 315
      removed outlier: 4.487A  pdb=" N   GLN E 315 " --> pdb=" O   LEU E 318 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU E 318 " --> pdb=" O   GLN E 315 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 322 through 326
      removed outlier: 4.408A  pdb=" N   ILE E 404 " --> pdb=" O   VAL E 411 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 340 through 344
      removed outlier: 4.711A  pdb=" N   VAL E 341 " --> pdb=" O   GLU E 357 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   GLU E 357 " --> pdb=" O   VAL E 341 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL E 354 " --> pdb=" O   TYR E 366 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   VAL E 356 " --> pdb=" O   SER E 364 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER E 364 " --> pdb=" O   VAL E 356 " (cutoff:3.500A)

    628 hydrogen bonds defined for protein.
    1839 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.91

  Time building geometry restraints manager: 3.26 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2854
        1.33 -     1.45: 1165
        1.45 -     1.57: 5142
        1.57 -     1.69: 10
        1.69 -     1.81: 52
  Bond restraints: 9223
  Sorted by residual:
  bond pdb=" N   VAL C 185 "
       pdb=" CA  VAL C 185 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.19e-02 7.06e+03 9.58e+00
  bond pdb=" N   VAL C 186 "
       pdb=" CA  VAL C 186 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.23e-02 6.61e+03 9.06e+00
  bond pdb=" N   VAL C 183 "
       pdb=" CA  VAL C 183 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.72e+00
  bond pdb=" N   ILE C 121 "
       pdb=" CA  ILE C 121 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 8.02e+00
  bond pdb=" N   ILE C 211 "
       pdb=" CA  ILE C 211 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.96e+00
  ... (remaining 9218 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 12395
        2.48 -     4.95: 214
        4.95 -     7.43: 23
        7.43 -     9.90: 3
        9.90 -    12.38: 2
  Bond angle restraints: 12637
  Sorted by residual:
  angle pdb=" PB  ATP B 301 "
        pdb=" O3B ATP B 301 "
        pdb=" PG  ATP B 301 "
      ideal   model   delta    sigma   weight residual
     139.87  129.08   10.79 1.00e+00 1.00e+00 1.16e+02
  angle pdb=" PB  ATP A 301 "
        pdb=" O3B ATP A 301 "
        pdb=" PG  ATP A 301 "
      ideal   model   delta    sigma   weight residual
     139.87  130.49    9.38 1.00e+00 1.00e+00 8.80e+01
  angle pdb=" N   ALA C 225 "
        pdb=" CA  ALA C 225 "
        pdb=" C   ALA C 225 "
      ideal   model   delta    sigma   weight residual
     114.62  108.03    6.59 1.14e+00 7.69e-01 3.34e+01
  angle pdb=" PA  ATP B 301 "
        pdb=" O3A ATP B 301 "
        pdb=" PB  ATP B 301 "
      ideal   model   delta    sigma   weight residual
     136.83  131.79    5.04 1.00e+00 1.00e+00 2.54e+01
  angle pdb=" N   VAL C 100 "
        pdb=" CA  VAL C 100 "
        pdb=" C   VAL C 100 "
      ideal   model   delta    sigma   weight residual
     112.96  108.55    4.41 1.00e+00 1.00e+00 1.95e+01
  ... (remaining 12632 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 4856
       16.99 -    33.98: 379
       33.98 -    50.97: 158
       50.97 -    67.95: 37
       67.95 -    84.94: 8
  Dihedral angle restraints: 5438
    sinusoidal: 1414
      harmonic: 4024
  Sorted by residual:
  dihedral pdb=" CA  GLU E 114 "
           pdb=" C   GLU E 114 "
           pdb=" N   ARG E 115 "
           pdb=" CA  ARG E 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.16   26.84     0      5.00e+00 4.00e-02 2.88e+01
  dihedral pdb=" CA  HIS A 195 "
           pdb=" C   HIS A 195 "
           pdb=" N   ASP A 196 "
           pdb=" CA  ASP A 196 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.77   22.23     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  SER D 264 "
           pdb=" C   SER D 264 "
           pdb=" N   ILE D 265 "
           pdb=" CA  ILE D 265 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.84   22.16     0      5.00e+00 4.00e-02 1.96e+01
  ... (remaining 5435 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1355
       0.066 -    0.131: 173
       0.131 -    0.197: 28
       0.197 -    0.262: 4
       0.262 -    0.328: 2
  Chirality restraints: 1562
  Sorted by residual:
  chirality pdb=" CB  THR C 360 "
            pdb=" CA  THR C 360 "
            pdb=" OG1 THR C 360 "
            pdb=" CG2 THR C 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.22    0.33 2.00e-01 2.50e+01 2.69e+00
  chirality pdb=" CB  VAL B  96 "
            pdb=" CA  VAL B  96 "
            pdb=" CG1 VAL B  96 "
            pdb=" CG2 VAL B  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  LEU C 198 "
            pdb=" N   LEU C 198 "
            pdb=" C   LEU C 198 "
            pdb=" CB  LEU C 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 1559 not shown)

  Planarity restraints: 1674
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 110 "    0.022 2.00e-02 2.50e+03   4.44e-02 1.97e+01
        pdb=" C   LYS E 110 "   -0.077 2.00e-02 2.50e+03
        pdb=" O   LYS E 110 "    0.028 2.00e-02 2.50e+03
        pdb=" N   ALA E 111 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 280 "    0.060 5.00e-02 4.00e+02   9.00e-02 1.29e+01
        pdb=" N   PRO D 281 "   -0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO D 281 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO D 281 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA E 104 "   -0.015 2.00e-02 2.50e+03   2.97e-02 8.84e+00
        pdb=" C   ALA E 104 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ALA E 104 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LYS E 105 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1671 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 104
        2.64 -     3.21: 8615
        3.21 -     3.77: 13968
        3.77 -     4.34: 17617
        4.34 -     4.90: 29660
  Nonbonded interactions: 69964
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 139 "
            pdb=" OE1 GLU A 142 "
     model   vdw
     2.075 3.040
  nonbonded pdb=" O   ASP A 169 "
            pdb=" OG  SER A 173 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" NH2 ARG A  79 "
            pdb=" O   GLY D 272 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" O   ASP C  76 "
            pdb=" OG  SER C  79 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OH  TYR B  11 "
            pdb=" OG1 THR B  43 "
     model   vdw
     2.244 3.040
  ... (remaining 69959 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 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 196 or (resid 197 through 198 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 199 through 218 or  \ 
resid 301))
  selection = (chain 'B' and (resid 1 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 name CA or name \ 
 C or name O or name CB )) or resid 71 through 218 or resid 301))
}
ncs_group {
  reference = (chain 'C' and ((resid 63 through 65 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 66 through 74 or (resid 75 through 76 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 77 through 220 or (resid 221 thro \ 
ugh 223 and (name N or name CA or name C or name O or name CB )) or resid 224 th \ 
rough 226 or (resid 227 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 228 through 229 or (resid 230 through 231 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 232 or (resid 233 through 234 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 235 through 307 or (resid  \ 
308 through 319 and (name N or name CA or name C or name O or name CB )) or (res \ 
id 320 through 326 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 327 through 331 or (resid 332 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 333 through 353 or (resid 354 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 355 through 359 or (resid 360 through 361 a \ 
nd (name N or name CA or name C or name O or name CB ))))
  selection = (chain 'D' and (resid 63 through 75 or (resid 76 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 77 through 105 or (resid 106 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 107 through 108 or (resid 109  \ 
through 116 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 
7 through 218 or (resid 219 through 223 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 224 through 233 or (resid 234 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 235 through 256 or (resid 257 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 258 through 262 or (re \ 
sid 263 and (name N or name CA or name C or name O or name CB )) or resid 264 th \ 
rough 301 or (resid 302 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 303 through 333 or (resid 334 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 335 through 361))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             669.830
  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:             0.020
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     31.600
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  705.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
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      :  0.007   0.063   9223  Z= 0.338
  Angle     :  0.798  12.378  12637  Z= 0.487
  Chirality :  0.050   0.328   1562
  Planarity :  0.005   0.090   1674
  Dihedral  : 16.177  84.942   2846
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  :  9.62 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 27.36 %
    Favored  : 71.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.23), residues: 1416
  helix:  0.81 (0.19), residues: 766
  sheet: -2.27 (0.51), residues: 68
  loop : -2.46 (0.25), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 345 
 HIS   0.006   0.001   HIS A 195 
 PHE   0.018   0.002   PHE B  23 
 TYR   0.008   0.001   TYR C  68 
 ARG   0.004   0.001   ARG C 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16783 (  628)
  hydrogen bonds       : angle       6.80848 ( 1839)
  covalent geometry    : bond        0.00667 ( 9223)
  covalent geometry    : angle       0.79838 (12637)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 1.153 
Fit side-chains
REVERT: A   71 ASN cc_start: 0.8147 (m-40) cc_final: 0.7845 (t0)
REVERT: C  306 LEU cc_start: 0.6695 (mt) cc_final: 0.6360 (pp)
  outliers start: 9
  outliers final: 2
  residues processed: 139
  average time/residue: 0.3207
  time to fit residues: 56.4483
Evaluate side-chains
  104 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  221 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    9.9990
   chunk 104 optimal weight:   10.0000
   chunk 58 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 55 optimal weight:    8.9990
   chunk 108 optimal weight:    7.9990
   chunk 41 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9990
   chunk 80 optimal weight:   20.0000
   chunk 125 optimal weight:    0.0970
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  71 HIS
** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.225281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.187166 restraints weight = 39703.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.4133 rms_B_bonded: 3.22
r_work: 0.3374 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9223  Z= 0.196
  Angle     :  0.669  13.488  12637  Z= 0.343
  Chirality :  0.042   0.215   1562
  Planarity :  0.004   0.057   1674
  Dihedral  :  8.576  85.367   1549
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  8.26 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 22.96 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.22), residues: 1416
  helix:  1.21 (0.19), residues: 766
  sheet: -2.65 (0.53), residues: 67
  loop : -2.41 (0.24), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  60 
 HIS   0.004   0.001   HIS B 214 
 PHE   0.012   0.002   PHE A  23 
 TYR   0.019   0.001   TYR C 105 
 ARG   0.005   0.001   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05652 (  628)
  hydrogen bonds       : angle       5.31902 ( 1839)
  covalent geometry    : bond        0.00449 ( 9223)
  covalent geometry    : angle       0.66858 (12637)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 114
  time to evaluate  : 0.941 
Fit side-chains
REVERT: A   71 ASN cc_start: 0.8468 (m-40) cc_final: 0.7732 (t0)
REVERT: A   83 MET cc_start: 0.8573 (ptt) cc_final: 0.7853 (ttt)
REVERT: A   84 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7693 (pt)
REVERT: B   53 ARG cc_start: 0.8743 (ttm170) cc_final: 0.8386 (mtm180)
REVERT: C   68 TYR cc_start: 0.7929 (t80) cc_final: 0.7654 (t80)
REVERT: C  319 PHE cc_start: 0.6249 (t80) cc_final: 0.5899 (t80)
REVERT: D   79 SER cc_start: 0.8560 (p) cc_final: 0.8354 (p)
REVERT: D  241 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7497 (mp)
REVERT: D  268 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7844 (tt0)
REVERT: D  302 GLU cc_start: 0.6419 (tm-30) cc_final: 0.6191 (tp30)
  outliers start: 38
  outliers final: 21
  residues processed: 144
  average time/residue: 0.2378
  time to fit residues: 45.9842
Evaluate side-chains
  128 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  261 ARG
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 136 optimal weight:   50.0000
   chunk 35 optimal weight:    0.3980
   chunk 85 optimal weight:   20.0000
   chunk 75 optimal weight:    2.9990
   chunk 119 optimal weight:    5.9990
   chunk 130 optimal weight:   50.0000
   chunk 24 optimal weight:    0.9980
   chunk 8 optimal weight:    0.4980
   chunk 23 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   chunk 88 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.221731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.186389 restraints weight = 36875.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.4125 rms_B_bonded: 3.08
r_work: 0.3368 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3357
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3357
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9223  Z= 0.189
  Angle     :  0.629  11.463  12637  Z= 0.321
  Chirality :  0.041   0.174   1562
  Planarity :  0.004   0.054   1674
  Dihedral  :  8.499  86.734   1547
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  7.55 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  7.49 %
    Allowed  : 20.68 %
    Favored  : 71.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.23), residues: 1416
  helix:  1.47 (0.19), residues: 770
  sheet: -1.74 (0.54), residues: 68
  loop : -2.23 (0.25), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 345 
 HIS   0.004   0.001   HIS B 214 
 PHE   0.020   0.002   PHE C 247 
 TYR   0.007   0.001   TYR B 205 
 ARG   0.004   0.001   ARG D 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05357 (  628)
  hydrogen bonds       : angle       5.01141 ( 1839)
  covalent geometry    : bond        0.00445 ( 9223)
  covalent geometry    : angle       0.62936 (12637)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 106
  time to evaluate  : 1.048 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8491 (ptt) cc_final: 0.7716 (ttt)
REVERT: A   84 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7681 (mp)
REVERT: A  195 HIS cc_start: 0.8100 (OUTLIER) cc_final: 0.7766 (p-80)
REVERT: A  200 ILE cc_start: 0.8632 (pt) cc_final: 0.8355 (pt)
REVERT: A  208 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8243 (mt)
REVERT: C   68 TYR cc_start: 0.7968 (t80) cc_final: 0.7586 (t80)
REVERT: C  355 HIS cc_start: 0.6514 (OUTLIER) cc_final: 0.6190 (t-90)
REVERT: D  241 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7527 (mp)
REVERT: D  268 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7737 (tt0)
  outliers start: 46
  outliers final: 26
  residues processed: 140
  average time/residue: 0.2407
  time to fit residues: 45.5772
Evaluate side-chains
  132 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 100
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  261 ARG
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  325 ILE
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 105 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 106 optimal weight:    6.9990
   chunk 8 optimal weight:    0.4980
   chunk 64 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9980
   chunk 63 optimal weight:    0.2980
   chunk 16 optimal weight:    0.4980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 216 HIS
D 107 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.223396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.181120 restraints weight = 25992.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.4047 rms_B_bonded: 7.25
r_work: 0.3078 rms_B_bonded: 5.89 restraints_weight: 2.0000
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3050
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3050
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.3184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9223  Z= 0.160
  Angle     :  0.587  11.942  12637  Z= 0.301
  Chirality :  0.040   0.183   1562
  Planarity :  0.004   0.052   1674
  Dihedral  :  8.085  88.669   1547
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  7.19 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 22.64 %
    Favored  : 71.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.23), residues: 1416
  helix:  1.59 (0.19), residues: 777
  sheet: -1.92 (0.53), residues: 80
  loop : -2.14 (0.25), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 345 
 HIS   0.003   0.001   HIS B 214 
 PHE   0.029   0.001   PHE C 247 
 TYR   0.006   0.001   TYR C 102 
 ARG   0.002   0.000   ARG A 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04845 (  628)
  hydrogen bonds       : angle       4.81105 ( 1839)
  covalent geometry    : bond        0.00365 ( 9223)
  covalent geometry    : angle       0.58691 (12637)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 105
  time to evaluate  : 1.000 
Fit side-chains
REVERT: A  183 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7628 (t80)
REVERT: A  200 ILE cc_start: 0.8669 (pt) cc_final: 0.8329 (pt)
REVERT: D  241 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7377 (mp)
REVERT: D  268 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7991 (tt0)
REVERT: D  302 GLU cc_start: 0.6431 (tp30) cc_final: 0.6153 (tp30)
  outliers start: 38
  outliers final: 24
  residues processed: 133
  average time/residue: 0.2378
  time to fit residues: 42.9175
Evaluate side-chains
  130 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 125 optimal weight:   40.0000
   chunk 19 optimal weight:    1.9990
   chunk 108 optimal weight:   20.0000
   chunk 97 optimal weight:    3.9990
   chunk 34 optimal weight:    0.1980
   chunk 127 optimal weight:   50.0000
   chunk 84 optimal weight:   20.0000
   chunk 5 optimal weight:    0.9990
   chunk 81 optimal weight:   20.0000
   chunk 98 optimal weight:    0.9990
   overall best weight:    1.6388

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.217846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.181802 restraints weight = 37381.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 3.07
r_work: 0.3304 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3286
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3286 r_free = 0.3286    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3286 r_free = 0.3286    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3286
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.084   9223  Z= 0.395
  Angle     :  0.823  11.318  12637  Z= 0.411
  Chirality :  0.051   0.296   1562
  Planarity :  0.005   0.059   1674
  Dihedral  :  8.809  82.382   1545
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  8.05 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  7.98 %
    Allowed  : 21.50 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.23), residues: 1416
  helix:  1.24 (0.19), residues: 774
  sheet: -1.78 (0.57), residues: 73
  loop : -2.32 (0.25), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.004   TRP D 345 
 HIS   0.008   0.003   HIS B 214 
 PHE   0.022   0.003   PHE A  23 
 TYR   0.012   0.002   TYR B 205 
 ARG   0.004   0.001   ARG B  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06803 (  628)
  hydrogen bonds       : angle       5.03222 ( 1839)
  covalent geometry    : bond        0.00991 ( 9223)
  covalent geometry    : angle       0.82252 (12637)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 110
  time to evaluate  : 1.055 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8571 (ptt) cc_final: 0.7776 (ttt)
REVERT: A  155 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7924 (pttt)
REVERT: A  208 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8389 (mt)
REVERT: B   51 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8608 (mm)
REVERT: B  207 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7540 (tmm)
REVERT: C  319 PHE cc_start: 0.5962 (t80) cc_final: 0.5571 (t80)
REVERT: D  241 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7299 (mp)
REVERT: D  268 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8015 (tt0)
  outliers start: 49
  outliers final: 29
  residues processed: 149
  average time/residue: 0.2266
  time to fit residues: 46.0100
Evaluate side-chains
  141 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 106
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  155 LYS
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  297 SER
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  330 PHE
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 48 optimal weight:   30.0000
   chunk 25 optimal weight:    0.5980
   chunk 92 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0980
   chunk 67 optimal weight:    4.9990
   chunk 114 optimal weight:   30.0000
   chunk 69 optimal weight:    0.5980
   chunk 128 optimal weight:    7.9990
   chunk 58 optimal weight:    0.6980
   chunk 102 optimal weight:   30.0000
   chunk 15 optimal weight:    0.3980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 216 HIS
B 216 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.222246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.187040 restraints weight = 38308.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.4134 rms_B_bonded: 3.05
r_work: 0.3384 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3353
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3353 r_free = 0.3353    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3353 r_free = 0.3353    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3353
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9223  Z= 0.160
  Angle     :  0.599  12.038  12637  Z= 0.307
  Chirality :  0.041   0.184   1562
  Planarity :  0.004   0.055   1674
  Dihedral  :  8.061  78.408   1545
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  7.26 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  6.84 %
    Allowed  : 22.48 %
    Favored  : 70.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.23), residues: 1416
  helix:  1.59 (0.19), residues: 776
  sheet: -1.42 (0.64), residues: 63
  loop : -2.20 (0.25), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 345 
 HIS   0.004   0.001   HIS C 355 
 PHE   0.020   0.001   PHE C 247 
 TYR   0.005   0.001   TYR C 102 
 ARG   0.003   0.000   ARG D 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04958 (  628)
  hydrogen bonds       : angle       4.75238 ( 1839)
  covalent geometry    : bond        0.00364 ( 9223)
  covalent geometry    : angle       0.59899 (12637)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 104
  time to evaluate  : 0.951 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8530 (ptt) cc_final: 0.7743 (ttt)
REVERT: A  174 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8277 (tp30)
REVERT: B  203 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8343 (mtt90)
REVERT: C   95 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8552 (tt)
REVERT: C  319 PHE cc_start: 0.5955 (t80) cc_final: 0.5486 (t80)
REVERT: D  241 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7493 (mp)
REVERT: D  268 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7920 (tt0)
  outliers start: 42
  outliers final: 28
  residues processed: 135
  average time/residue: 0.2415
  time to fit residues: 44.0615
Evaluate side-chains
  134 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 102
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  203 ARG
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 105 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 52 optimal weight:   30.0000
   chunk 132 optimal weight:   50.0000
   chunk 9 optimal weight:    0.0870
   chunk 24 optimal weight:    0.9990
   chunk 30 optimal weight:    0.1980
   chunk 32 optimal weight:    0.5980
   chunk 78 optimal weight:   20.0000
   chunk 113 optimal weight:   10.0000
   overall best weight:    0.7762

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.220891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.182096 restraints weight = 33618.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.4083 rms_B_bonded: 3.62
r_work: 0.3298 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3273
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3273
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.3779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9223  Z= 0.209
  Angle     :  0.647  11.899  12637  Z= 0.327
  Chirality :  0.043   0.202   1562
  Planarity :  0.004   0.055   1674
  Dihedral  :  8.223  83.191   1545
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  7.55 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  6.84 %
    Allowed  : 22.80 %
    Favored  : 70.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.23), residues: 1416
  helix:  1.66 (0.19), residues: 775
  sheet: -1.41 (0.60), residues: 73
  loop : -2.23 (0.25), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 345 
 HIS   0.004   0.001   HIS C 355 
 PHE   0.019   0.002   PHE C 247 
 TYR   0.007   0.001   TYR B 205 
 ARG   0.004   0.000   ARG D 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05312 (  628)
  hydrogen bonds       : angle       4.69755 ( 1839)
  covalent geometry    : bond        0.00504 ( 9223)
  covalent geometry    : angle       0.64668 (12637)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 102
  time to evaluate  : 1.707 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8622 (ptt) cc_final: 0.7798 (ttt)
REVERT: A   87 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8242 (m-30)
REVERT: A  183 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7516 (t80)
REVERT: B  203 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8337 (mtt90)
REVERT: C   95 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8529 (tt)
REVERT: C  319 PHE cc_start: 0.5877 (t80) cc_final: 0.5473 (t80)
REVERT: C  342 MET cc_start: 0.8642 (mmm) cc_final: 0.8376 (mmt)
REVERT: C  354 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7836 (tm-30)
REVERT: D  241 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7437 (mp)
REVERT: D  268 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7914 (tt0)
  outliers start: 42
  outliers final: 31
  residues processed: 136
  average time/residue: 0.2917
  time to fit residues: 54.2427
Evaluate side-chains
  139 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 102
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  203 ARG
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 11 optimal weight:    0.2980
   chunk 59 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 78 optimal weight:   20.0000
   chunk 94 optimal weight:    1.9990
   chunk 80 optimal weight:   30.0000
   chunk 132 optimal weight:   50.0000
   chunk 20 optimal weight:    0.6980
   chunk 8 optimal weight:    0.1980
   chunk 86 optimal weight:    7.9990
   chunk 56 optimal weight:   40.0000
   overall best weight:    0.7782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.220841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.181194 restraints weight = 37249.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.4073 rms_B_bonded: 3.62
r_work: 0.3300 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.3989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9223  Z= 0.211
  Angle     :  0.638  12.102  12637  Z= 0.322
  Chirality :  0.043   0.235   1562
  Planarity :  0.004   0.056   1674
  Dihedral  :  8.118  81.524   1545
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.12 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  6.84 %
    Allowed  : 22.96 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.23), residues: 1416
  helix:  1.76 (0.19), residues: 773
  sheet: -1.91 (0.53), residues: 91
  loop : -2.16 (0.25), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 345 
 HIS   0.006   0.001   HIS C 355 
 PHE   0.017   0.002   PHE C 247 
 TYR   0.007   0.001   TYR B 205 
 ARG   0.003   0.000   ARG D 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05191 (  628)
  hydrogen bonds       : angle       4.60330 ( 1839)
  covalent geometry    : bond        0.00512 ( 9223)
  covalent geometry    : angle       0.63751 (12637)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 103
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8611 (ptt) cc_final: 0.7792 (ttt)
REVERT: A   87 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8197 (m-30)
REVERT: B  203 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8350 (mtt90)
REVERT: C   95 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8544 (tt)
REVERT: C  269 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8197 (tttp)
REVERT: C  342 MET cc_start: 0.8630 (mmm) cc_final: 0.8355 (mmt)
REVERT: D  241 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7417 (mp)
REVERT: D  268 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7938 (tt0)
  outliers start: 42
  outliers final: 32
  residues processed: 136
  average time/residue: 0.2379
  time to fit residues: 43.4375
Evaluate side-chains
  140 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 102
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  203 ARG
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  269 LYS
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 56 optimal weight:   40.0000
   chunk 55 optimal weight:   20.0000
   chunk 59 optimal weight:    2.9990
   chunk 122 optimal weight:    9.9990
   chunk 35 optimal weight:    0.6980
   chunk 131 optimal weight:   30.0000
   chunk 31 optimal weight:    0.2980
   chunk 100 optimal weight:    6.9990
   chunk 77 optimal weight:   20.0000
   chunk 127 optimal weight:    0.0010
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.9388

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

Flipped N/Q/H residues before XYZ refinement:
D 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.219680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.167144 restraints weight = 31481.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 10.21
r_work: 0.2969 rms_B_bonded: 6.42 restraints_weight: 2.0000
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2935
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2935
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.4218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   9223  Z= 0.247
  Angle     :  0.682  11.965  12637  Z= 0.343
  Chirality :  0.044   0.259   1562
  Planarity :  0.004   0.056   1674
  Dihedral  :  8.408  88.433   1545
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.26 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  7.33 %
    Allowed  : 22.48 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.23), residues: 1416
  helix:  1.72 (0.19), residues: 779
  sheet: -1.39 (0.61), residues: 72
  loop : -2.24 (0.25), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D 345 
 HIS   0.006   0.001   HIS C 355 
 PHE   0.017   0.002   PHE C 247 
 TYR   0.009   0.001   TYR B 205 
 ARG   0.004   0.001   ARG D 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05584 (  628)
  hydrogen bonds       : angle       4.56557 ( 1839)
  covalent geometry    : bond        0.00611 ( 9223)
  covalent geometry    : angle       0.68216 (12637)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 102
  time to evaluate  : 0.947 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8870 (ptt) cc_final: 0.7845 (ttt)
REVERT: B  203 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8384 (mtt90)
REVERT: C   95 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8395 (tt)
REVERT: C  269 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8203 (tttp)
REVERT: C  306 LEU cc_start: 0.6752 (mt) cc_final: 0.5736 (pp)
REVERT: C  354 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7777 (tm-30)
REVERT: D  241 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7253 (mp)
REVERT: D  268 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8096 (tt0)
  outliers start: 45
  outliers final: 34
  residues processed: 137
  average time/residue: 0.2498
  time to fit residues: 45.7387
Evaluate side-chains
  140 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 101
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  203 ARG
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  269 LYS
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 99 optimal weight:    0.9990
   chunk 115 optimal weight:   50.0000
   chunk 27 optimal weight:    0.7980
   chunk 101 optimal weight:   30.0000
   chunk 108 optimal weight:    9.9990
   chunk 63 optimal weight:    0.1980
   chunk 88 optimal weight:    0.9980
   chunk 55 optimal weight:   40.0000
   chunk 3 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 110 optimal weight:   20.0000
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 214 HIS
B 216 HIS
D 266 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.221135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.185453 restraints weight = 37823.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.4116 rms_B_bonded: 3.06
r_work: 0.3364 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3332
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3332
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.4288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9223  Z= 0.191
  Angle     :  0.626  12.286  12637  Z= 0.318
  Chirality :  0.042   0.279   1562
  Planarity :  0.004   0.055   1674
  Dihedral  :  8.085  81.288   1545
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  6.77 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  6.68 %
    Allowed  : 23.13 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.23), residues: 1416
  helix:  1.83 (0.19), residues: 779
  sheet: -1.77 (0.54), residues: 90
  loop : -2.14 (0.25), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 345 
 HIS   0.005   0.001   HIS C 355 
 PHE   0.016   0.002   PHE C 247 
 TYR   0.006   0.001   TYR B 205 
 ARG   0.003   0.000   ARG B 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05004 (  628)
  hydrogen bonds       : angle       4.46667 ( 1839)
  covalent geometry    : bond        0.00461 ( 9223)
  covalent geometry    : angle       0.62619 (12637)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 103
  time to evaluate  : 1.005 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8554 (ptt) cc_final: 0.7760 (ttt)
REVERT: A   90 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8454 (pp)
REVERT: C   95 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8537 (tt)
REVERT: C  269 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8200 (tttp)
REVERT: C  306 LEU cc_start: 0.6892 (mt) cc_final: 0.5838 (pp)
REVERT: C  342 MET cc_start: 0.8572 (mmm) cc_final: 0.8317 (mmt)
REVERT: C  354 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7863 (tm-30)
REVERT: D  241 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7423 (mp)
REVERT: D  268 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7915 (tt0)
  outliers start: 41
  outliers final: 33
  residues processed: 136
  average time/residue: 0.2435
  time to fit residues: 44.6302
Evaluate side-chains
  140 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 102
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  269 LYS
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  297 SER
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 115 optimal weight:   50.0000
   chunk 59 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   chunk 39 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 82 optimal weight:   20.0000
   chunk 37 optimal weight:    0.1980
   chunk 118 optimal weight:    6.9990
   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 214 HIS
B 216 HIS
D 266 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.220507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.167543 restraints weight = 30688.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 10.40
r_work: 0.2968 rms_B_bonded: 6.54 restraints_weight: 2.0000
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.4358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9223  Z= 0.216
  Angle     :  0.651  12.567  12637  Z= 0.329
  Chirality :  0.043   0.277   1562
  Planarity :  0.004   0.056   1674
  Dihedral  :  8.128  82.859   1545
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  6.62 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  7.17 %
    Allowed  : 22.31 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.23), residues: 1416
  helix:  1.87 (0.19), residues: 773
  sheet: -1.79 (0.55), residues: 90
  loop : -2.15 (0.25), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 345 
 HIS   0.006   0.002   HIS C 355 
 PHE   0.016   0.002   PHE C 247 
 TYR   0.007   0.001   TYR B 205 
 ARG   0.003   0.000   ARG D 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05203 (  628)
  hydrogen bonds       : angle       4.45511 ( 1839)
  covalent geometry    : bond        0.00527 ( 9223)
  covalent geometry    : angle       0.65056 (12637)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8626.09 seconds
wall clock time: 152 minutes 25.75 seconds (9145.75 seconds total)