Starting phenix.real_space_refine
on Thu Sep 18 06:17:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uuu_64518/09_2025/9uuu_64518.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uuu_64518/09_2025/9uuu_64518.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uuu_64518/09_2025/9uuu_64518.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uuu_64518/09_2025/9uuu_64518.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uuu_64518/09_2025/9uuu_64518.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uuu_64518/09_2025/9uuu_64518.cif"
  }
  resolution = 3.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.074
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: 7
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     Fe      4      7.16       5
     P       6      5.49       5
     S      92      5.16       5
     C    9490      2.51       5
     N    2413      2.21       5
     O    2688      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14694
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 3416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 446, 3416
          Classifications: {'peptide': 446}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422}
    Chain: "B"
      Number of atoms: 2933
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 383, 2933
          Classifications: {'peptide': 383}
          Link IDs: {'PTRANS': 14, 'TRANS': 368}
    Chain: "C"
      Number of atoms: 1902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1902
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 7, 'TRANS': 243}
    Chain: "D"
      Number of atoms: 1580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1580
          Classifications: {'peptide': 206}
          Link IDs: {'PTRANS': 9, 'TRANS': 196}
    Chain: "E"
      Number of atoms: 1511
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1511
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 7, 'TRANS': 190}
    Chain: "F"
      Number of atoms: 3157
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 408, 3157
          Classifications: {'peptide': 408}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 24, 'TRANS': 383}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "B"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 58
          Unusual residues: {'FMN': 1, 'RBF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' CA': 1, 'FMN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'FES': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 101
          Unusual residues: {'FAD': 1, 'FES': 1, 'NAI': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8436  SG  CYS D  29      48.369  58.911  63.309  1.00 82.13           S

  Time building chain proxies: 3.58, per 1000 atoms: 0.24
  Number of scatterers: 14694
  At special positions: 0
  Unit cell: (91.52, 126.72, 154.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      4     26.01
     Ca      1     19.99
     S      92     16.00
     P       6     15.00
     O    2688      8.00
     N    2413      7.00
     C    9490      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: 1.27
  Conformation dependent library (CDL) restraints added in 634.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" FES D 301 "
        pdb="FE2  FES D 301 " - pdb=" SG  CYS D  29 "
        pdb="FE2  FES D 301 " - pdb=" SG  CYS E 120 "
        pdb="FE1  FES D 301 " - pdb=" SG  CYS E  26 "
      Number of angles added : 4


  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3416

  Finding SS restraints...
    Secondary structure from input PDB file:
      77 helices and 14 sheets defined
      50.4% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 83 through 85
      No H-bonds generated for 'chain 'A' and resid 83 through 85'
    Processing helix  chain 'A' and resid 107 through 113
      removed outlier: 3.706A  pdb=" N   LEU A 110 " --> pdb=" O   ALA A 107 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ALA A 111 " --> pdb=" O   ASN A 108 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   SER A 112 " --> pdb=" O   GLN A 109 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU A 113 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 107 through 113'
    Processing helix  chain 'A' and resid 114 through 126
    Processing helix  chain 'A' and resid 127 through 131
    Processing helix  chain 'A' and resid 162 through 168
      removed outlier: 3.771A  pdb=" N   VAL A 166 " --> pdb=" O   GLU A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 185
    Processing helix  chain 'A' and resid 219 through 228
    Processing helix  chain 'A' and resid 241 through 254
    Processing helix  chain 'A' and resid 282 through 287
    Processing helix  chain 'A' and resid 310 through 314
      removed outlier: 3.897A  pdb=" N   HIS A 313 " --> pdb=" O   THR A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 339
      removed outlier: 3.647A  pdb=" N   MET A 339 " --> pdb=" O   GLY A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 356
      removed outlier: 3.801A  pdb=" N   HIS A 354 " --> pdb=" O   PHE A 351 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU A 355 " --> pdb=" O   LEU A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 384
      removed outlier: 3.735A  pdb=" N   VAL A 383 " --> pdb=" O   ASN A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 400
    Processing helix  chain 'A' and resid 401 through 409
    Processing helix  chain 'A' and resid 418 through 424
    Processing helix  chain 'A' and resid 430 through 446
      removed outlier: 3.930A  pdb=" N   LEU A 434 " --> pdb=" O   GLU A 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 64
      removed outlier: 3.936A  pdb=" N   VAL B  64 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 87
    Processing helix  chain 'B' and resid 89 through 97
    Processing helix  chain 'B' and resid 99 through 108
      removed outlier: 3.773A  pdb=" N   THR B 105 " --> pdb=" O   HIS B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 151
      removed outlier: 3.674A  pdb=" N   TYR B 128 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
      Proline residue:  B 131  - end of helix
    Processing helix  chain 'B' and resid 158 through 168
      removed outlier: 3.751A  pdb=" N   ILE B 164 " --> pdb=" O   PHE B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 189
    Processing helix  chain 'B' and resid 203 through 216
      removed outlier: 3.567A  pdb=" N   GLY B 208 " --> pdb=" O   PRO B 204 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ARG B 209 " --> pdb=" O   ALA B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 245
      removed outlier: 3.556A  pdb=" N   TRP B 241 " --> pdb=" O   ALA B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 249
      removed outlier: 3.771A  pdb=" N   LEU B 249 " --> pdb=" O   ALA B 246 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 246 through 249'
    Processing helix  chain 'B' and resid 259 through 266
    Processing helix  chain 'B' and resid 276 through 290
      removed outlier: 4.251A  pdb=" N   PHE B 286 " --> pdb=" O   ILE B 282 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ILE B 287 " --> pdb=" O   GLY B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 316
    Processing helix  chain 'B' and resid 326 through 331
    Processing helix  chain 'B' and resid 335 through 343
    Processing helix  chain 'B' and resid 353 through 375
      removed outlier: 3.906A  pdb=" N   TRP B 358 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ALA B 359 " --> pdb=" O   SER B 355 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASN B 375 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 410
      removed outlier: 4.580A  pdb=" N   LEU B 391 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   PHE B 392 " --> pdb=" O   PHE B 388 " (cutoff:3.500A)
      Proline residue:  B 394  - end of helix
    Processing helix  chain 'C' and resid 7 through 32
    Processing helix  chain 'C' and resid 33 through 53
      removed outlier: 4.131A  pdb=" N   LYS C  45 " --> pdb=" O   ALA C  41 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   LYS C  48 " --> pdb=" O   ASP C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 70
      removed outlier: 3.501A  pdb=" N   LYS C  69 " --> pdb=" O   GLU C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'C' and resid 177 through 181
      removed outlier: 3.937A  pdb=" N   VAL C 180 " --> pdb=" O   GLY C 177 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU C 181 " --> pdb=" O   GLY C 178 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 177 through 181'
    Processing helix  chain 'C' and resid 182 through 187
    Processing helix  chain 'C' and resid 224 through 239
      removed outlier: 3.742A  pdb=" N   GLY C 230 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   PHE C 235 " --> pdb=" O   VAL C 231 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 254
    Processing helix  chain 'D' and resid 6 through 13
    Processing helix  chain 'D' and resid 28 through 35
      removed outlier: 4.204A  pdb=" N   THR D  35 " --> pdb=" O   ALA D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 62
    Processing helix  chain 'D' and resid 70 through 94
    Processing helix  chain 'D' and resid 94 through 101
    Processing helix  chain 'D' and resid 111 through 121
      removed outlier: 4.034A  pdb=" N   MET D 115 " --> pdb=" O   ASN D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 158
      removed outlier: 4.140A  pdb=" N   VAL D 144 " --> pdb=" O   GLY D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 183 through 202
      removed outlier: 3.975A  pdb=" N   ALA D 187 " --> pdb=" O   LEU D 183 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 203 through 206
      removed outlier: 4.008A  pdb=" N   VAL D 206 " --> pdb=" O   PRO D 203 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 203 through 206'
    Processing helix  chain 'E' and resid 2 through 13
    Processing helix  chain 'E' and resid 24 through 31
    Processing helix  chain 'E' and resid 34 through 63
      Proline residue:  E  54  - end of helix
    Processing helix  chain 'E' and resid 78 through 101
      removed outlier: 4.409A  pdb=" N   PHE E 101 " --> pdb=" O   ILE E  97 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 117
      removed outlier: 3.886A  pdb=" N   PHE E 112 " --> pdb=" O   LEU E 109 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU E 113 " --> pdb=" O   GLY E 110 " (cutoff:3.500A)
      Proline residue:  E 114  - end of helix
      removed outlier: 3.727A  pdb=" N   THR E 117 " --> pdb=" O   PRO E 114 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 109 through 117'
    Processing helix  chain 'E' and resid 119 through 133
      removed outlier: 3.951A  pdb=" N   PHE E 123 " --> pdb=" O   ASN E 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 135 through 164
    Processing helix  chain 'E' and resid 170 through 174
    Processing helix  chain 'E' and resid 175 through 190
    Processing helix  chain 'E' and resid 191 through 194
      removed outlier: 3.525A  pdb=" N   SER E 194 " --> pdb=" O   MET E 191 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 191 through 194'
    Processing helix  chain 'F' and resid 2 through 30
      removed outlier: 3.572A  pdb=" N   LEU F  18 " --> pdb=" O   ILE F  14 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 38 through 42
    Processing helix  chain 'F' and resid 55 through 63
      removed outlier: 3.800A  pdb=" N   LEU F  59 " --> pdb=" O   LEU F  55 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA F  60 " --> pdb=" O   LEU F  56 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 91 through 98
    Processing helix  chain 'F' and resid 99 through 104
    Processing helix  chain 'F' and resid 178 through 182
    Processing helix  chain 'F' and resid 187 through 195
      removed outlier: 4.351A  pdb=" N   ASP F 191 " --> pdb=" O   LYS F 187 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 196 through 200
      removed outlier: 3.981A  pdb=" N   TYR F 200 " --> pdb=" O   LEU F 197 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 243 through 251
      removed outlier: 4.095A  pdb=" N   SER F 251 " --> pdb=" O   SER F 247 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 284 through 298
      removed outlier: 4.417A  pdb=" N   MET F 288 " --> pdb=" O   GLY F 284 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 319 through 330
      removed outlier: 3.970A  pdb=" N   PHE F 323 " --> pdb=" O   TYR F 319 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 343 through 347
      removed outlier: 3.736A  pdb=" N   ASP F 346 " --> pdb=" O   GLN F 343 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 354 through 363
      removed outlier: 3.548A  pdb=" N   TYR F 360 " --> pdb=" O   HIS F 356 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 369 through 373
    Processing helix  chain 'F' and resid 381 through 393
      removed outlier: 4.665A  pdb=" N   VAL F 387 " --> pdb=" O   MET F 383 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 397 through 399
      No H-bonds generated for 'chain 'F' and resid 397 through 399'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3
      removed outlier: 6.889A  pdb=" N   ILE A 149 " --> pdb=" O   TYR A 190 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   CYS A 192 " --> pdb=" O   ILE A 149 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   VAL A 151 " --> pdb=" O   CYS A 192 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   ALA A 148 " --> pdb=" O   TRP A 237 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   ILE A 239 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   PHE A 150 " --> pdb=" O   ILE A 239 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 21
      removed outlier: 5.937A  pdb=" N   GLN A 322 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   THR A 307 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 30
      removed outlier: 6.830A  pdb=" N   LEU A  87 " --> pdb=" O   ARG A  81 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ARG A  81 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   SER A  89 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   ILE A  79 " --> pdb=" O   SER A  89 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   VAL A  91 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43
      removed outlier: 3.678A  pdb=" N   THR A  42 " --> pdb=" O   GLU A  59 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   PHE A  68 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 77
      removed outlier: 3.738A  pdb=" N   VAL C 124 " --> pdb=" O   ARG C  74 " (cutoff:3.500A)
      removed outlier: 15.566A  pdb=" N   VAL C 121 " --> pdb=" O   VAL C 140 " (cutoff:3.500A)
      removed outlier: 11.887A  pdb=" N   VAL C 140 " --> pdb=" O   VAL C 121 " (cutoff:3.500A)
      removed outlier: 9.369A  pdb=" N   VAL C 123 " --> pdb=" O   LEU C 138 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   LEU C 138 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   TYR C 125 " --> pdb=" O   VAL C 136 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   VAL C 136 " --> pdb=" O   TYR C 125 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   VAL C 127 " --> pdb=" O   SER C 134 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   MET C 148 " --> pdb=" O   GLU C 169 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   GLU C 169 " --> pdb=" O   MET C 148 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   TYR C 150 " --> pdb=" O   TYR C 167 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   TYR C 167 " --> pdb=" O   TYR C 150 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   PHE C 152 " --> pdb=" O   LEU C 165 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   LEU C 165 " --> pdb=" O   PHE C 152 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ALA C 154 " --> pdb=" O   SER C 163 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 105
      removed outlier: 3.643A  pdb=" N   ARG C 118 " --> pdb=" O   ILE C 104 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 206
      removed outlier: 6.701A  pdb=" N   LYS C 204 " --> pdb=" O   VAL C 218 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 160
    Processing sheet with id=AA9, first strand: chain 'F' and resid 35 through 37
    Processing sheet with id=AB1, first strand: chain 'F' and resid 80 through 81
    Processing sheet with id=AB2, first strand: chain 'F' and resid 151 through 153
      removed outlier: 7.342A  pdb=" N   LYS F 151 " --> pdb=" O   ILE F 138 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 148 through 149
    Processing sheet with id=AB4, first strand: chain 'F' and resid 276 through 279
      removed outlier: 6.402A  pdb=" N   TYR F 375 " --> pdb=" O   LEU F 402 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 307 through 311
      removed outlier: 3.591A  pdb=" N   HIS F 336 " --> pdb=" O   TYR F 307 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA F 338 " --> pdb=" O   TYR F 309 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   TYR F 351 " --> pdb=" O   CYS F 337 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU F 339 " --> pdb=" O   TYR F 351 " (cutoff:3.500A)

    671 hydrogen bonds defined for protein.
    1938 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: 1.96

  Time building geometry restraints manager: 1.65 seconds

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

  Histogram of bond lengths:
        1.17 -     1.38: 5632
        1.38 -     1.58: 9231
        1.58 -     1.79: 77
        1.79 -     1.99: 87
        1.99 -     2.20: 8
  Bond restraints: 15035
  Sorted by residual:
  bond pdb=" C2B NAI F 503 "
       pdb=" C3B NAI F 503 "
    ideal  model  delta    sigma   weight residual
    1.530  1.236  0.294 2.00e-02 2.50e+03 2.16e+02
  bond pdb=" C3D NAI F 503 "
       pdb=" C4D NAI F 503 "
    ideal  model  delta    sigma   weight residual
    1.524  1.274  0.250 2.00e-02 2.50e+03 1.56e+02
  bond pdb=" C1D NAI F 503 "
       pdb=" C2D NAI F 503 "
    ideal  model  delta    sigma   weight residual
    1.528  1.278  0.250 2.00e-02 2.50e+03 1.56e+02
  bond pdb=" C5N NAI F 503 "
       pdb=" C6N NAI F 503 "
    ideal  model  delta    sigma   weight residual
    1.330  1.531 -0.201 2.00e-02 2.50e+03 1.01e+02
  bond pdb=" C2N NAI F 503 "
       pdb=" C3N NAI F 503 "
    ideal  model  delta    sigma   weight residual
    1.348  1.523 -0.175 2.00e-02 2.50e+03 7.62e+01
  ... (remaining 15030 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.06: 20266
        4.06 -     8.12: 126
        8.12 -    12.18: 12
       12.18 -    16.24: 11
       16.24 -    20.30: 3
  Bond angle restraints: 20418
  Sorted by residual:
  angle pdb=" S1  FES D 301 "
        pdb="FE2  FES D 301 "
        pdb=" S2  FES D 301 "
      ideal   model   delta    sigma   weight residual
     104.33   90.56   13.77 1.14e+00 7.69e-01 1.46e+02
  angle pdb="FE1  FES D 301 "
        pdb=" S2  FES D 301 "
        pdb="FE2  FES D 301 "
      ideal   model   delta    sigma   weight residual
      75.66   89.12  -13.46 1.14e+00 7.69e-01 1.39e+02
  angle pdb=" S1  FES D 301 "
        pdb="FE1  FES D 301 "
        pdb=" S2  FES D 301 "
      ideal   model   delta    sigma   weight residual
     104.33   90.36   13.97 1.20e+00 6.94e-01 1.36e+02
  angle pdb=" S1  FES F 501 "
        pdb="FE2  FES F 501 "
        pdb=" S2  FES F 501 "
      ideal   model   delta    sigma   weight residual
     104.33   91.15   13.18 1.14e+00 7.69e-01 1.34e+02
  angle pdb="FE1  FES F 501 "
        pdb=" S2  FES F 501 "
        pdb="FE2  FES F 501 "
      ideal   model   delta    sigma   weight residual
      75.66   88.77  -13.11 1.14e+00 7.69e-01 1.32e+02
  ... (remaining 20413 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.00: 8071
       20.00 -    39.99: 660
       39.99 -    59.99: 116
       59.99 -    79.99: 23
       79.99 -    99.98: 10
  Dihedral angle restraints: 8880
    sinusoidal: 3525
      harmonic: 5355
  Sorted by residual:
  dihedral pdb=" CA  VAL F  66 "
           pdb=" C   VAL F  66 "
           pdb=" N   SER F  67 "
           pdb=" CA  SER F  67 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -132.29  -47.71     0      5.00e+00 4.00e-02 9.10e+01
  dihedral pdb=" CA  ARG B  43 "
           pdb=" C   ARG B  43 "
           pdb=" N   SER B  44 "
           pdb=" CA  SER B  44 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.24  -29.76     0      5.00e+00 4.00e-02 3.54e+01
  dihedral pdb=" CA  PHE F  65 "
           pdb=" C   PHE F  65 "
           pdb=" N   VAL F  66 "
           pdb=" CA  VAL F  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.91   29.09     0      5.00e+00 4.00e-02 3.39e+01
  ... (remaining 8877 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1893
       0.067 -    0.133: 373
       0.133 -    0.199: 36
       0.199 -    0.266: 2
       0.266 -    0.332: 2
  Chirality restraints: 2306
  Sorted by residual:
  chirality pdb=" C3B NAI F 503 "
            pdb=" C2B NAI F 503 "
            pdb=" C4B NAI F 503 "
            pdb=" O3B NAI F 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.72   -2.38   -0.33 2.00e-01 2.50e+01 2.76e+00
  chirality pdb=" C3D NAI F 503 "
            pdb=" C2D NAI F 503 "
            pdb=" C4D NAI F 503 "
            pdb=" O3D NAI F 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.42   -0.29 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" C4' RBF B 502 "
            pdb=" C3' RBF B 502 "
            pdb=" C5' RBF B 502 "
            pdb=" O4' RBF B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.52    0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 2303 not shown)

  Planarity restraints: 2567
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  66 "   -0.018 2.00e-02 2.50e+03   3.70e-02 1.37e+01
        pdb=" C   VAL F  66 "    0.064 2.00e-02 2.50e+03
        pdb=" O   VAL F  66 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   SER F  67 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO E 103 "    0.060 5.00e-02 4.00e+02   9.04e-02 1.31e+01
        pdb=" N   PRO E 104 "   -0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO E 104 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO E 104 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F 286 "   -0.049 5.00e-02 4.00e+02   7.41e-02 8.78e+00
        pdb=" N   PRO F 287 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO F 287 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO F 287 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 2564 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 3578
        2.79 -     3.31: 13258
        3.31 -     3.84: 23747
        3.84 -     4.37: 27447
        4.37 -     4.90: 48754
  Nonbonded interactions: 116784
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 179 "
            pdb=" OG  SER A 201 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   GLN A 249 "
            pdb=" OG1 THR A 253 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   PHE E  28 "
            pdb=" OG  SER E  32 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" NE1 TRP B 260 "
            pdb=" O   HIS B 328 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" OG1 THR B 236 "
            pdb=" O3P FMN B 501 "
     model   vdw
     2.278 3.040
  ... (remaining 116779 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     15.320
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
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      :  0.014   0.737  15038  Z= 0.507
  Angle     :  1.054  26.611  20422  Z= 0.568
  Chirality :  0.053   0.332   2306
  Planarity :  0.007   0.090   2567
  Dihedral  : 15.329  99.983   5464
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.59 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.13 (0.16), residues: 1880
  helix: -1.39 (0.15), residues: 844
  sheet: -3.16 (0.36), residues: 142
  loop : -2.56 (0.16), residues: 894

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 209 
 TYR   0.021   0.002   TYR F 307 
 PHE   0.042   0.002   PHE B 323 
 TRP   0.030   0.002   TRP B 103 
 HIS   0.005   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00983 (15035)
  covalent geometry    : angle       1.01843 (20418)
  hydrogen bonds       : bond        0.13329 (  671)
  hydrogen bonds       : angle       6.21891 ( 1938)
  metal coordination   : bond        0.70344 (    3)
  metal coordination   : angle      19.49890 (    4)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A    5 LYS cc_start: 0.8520 (mttp) cc_final: 0.7965 (mttm)
REVERT: A   22 ASP cc_start: 0.7603 (t0) cc_final: 0.7361 (t0)
REVERT: B   42 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7666 (mtmm)
REVERT: B  151 ARG cc_start: 0.5517 (mmm160) cc_final: 0.4355 (ptp-110)
REVERT: B  152 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8083 (tppt)
REVERT: B  156 ASN cc_start: 0.8075 (p0) cc_final: 0.7760 (p0)
REVERT: B  302 MET cc_start: 0.8069 (tpp) cc_final: 0.7859 (tpt)
REVERT: B  367 MET cc_start: 0.8465 (mmm) cc_final: 0.8041 (mmt)
REVERT: C   51 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7833 (tm-30)
REVERT: D   18 ASN cc_start: 0.8149 (t0) cc_final: 0.7546 (t0)
REVERT: D  119 GLU cc_start: 0.8596 (tp30) cc_final: 0.8304 (tp30)
REVERT: D  139 LEU cc_start: 0.7751 (mt) cc_final: 0.7478 (mp)
REVERT: E   15 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7837 (mt-10)
REVERT: E   73 VAL cc_start: 0.8982 (t) cc_final: 0.8704 (p)
REVERT: F   10 MET cc_start: 0.8211 (mmm) cc_final: 0.7891 (mmt)
REVERT: F  276 MET cc_start: 0.7799 (mtt) cc_final: 0.7437 (mtp)
REVERT: F  285 MET cc_start: 0.6171 (tmm) cc_final: 0.5856 (tmm)
REVERT: F  319 TYR cc_start: 0.7092 (m-10) cc_final: 0.6667 (m-10)
REVERT: F  336 HIS cc_start: 0.8346 (m-70) cc_final: 0.7758 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.1269
  time to fit residues: 38.1667
Evaluate side-chains
  160 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 98 optimal weight:    0.3980
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:   10.0000
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
A  44 HIS
A 242 GLN
A 343 ASN
B  84 ASN
B 243 GLN
B 313 ASN
C 110 GLN
D  68 ASN
D 171 ASN
F  40 ASN
** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 362 ASN
** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.161778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.108532 restraints weight = 18735.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.92
r_work: 0.3091 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.1014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  15038  Z= 0.190
  Angle     :  0.613  10.686  20422  Z= 0.319
  Chirality :  0.044   0.152   2306
  Planarity :  0.006   0.078   2567
  Dihedral  :  8.743  81.515   2151
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.53 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.56 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.68 (0.18), residues: 1880
  helix:  0.15 (0.18), residues: 845
  sheet: -2.91 (0.37), residues: 151
  loop : -2.06 (0.19), residues: 884

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 118 
 TYR   0.018   0.001   TYR F 307 
 PHE   0.028   0.002   PHE F 182 
 TRP   0.028   0.002   TRP F 250 
 HIS   0.004   0.001   HIS F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (15035)
  covalent geometry    : angle       0.61052 (20418)
  hydrogen bonds       : bond        0.05164 (  671)
  hydrogen bonds       : angle       4.96674 ( 1938)
  metal coordination   : bond        0.02964 (    3)
  metal coordination   : angle       3.90569 (    4)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 169
  time to evaluate  : 0.532 
Fit side-chains
REVERT: A    5 LYS cc_start: 0.8721 (mttp) cc_final: 0.8138 (mttm)
REVERT: B   42 LYS cc_start: 0.8357 (mmtt) cc_final: 0.7856 (mtmm)
REVERT: B  151 ARG cc_start: 0.5524 (mmm160) cc_final: 0.4409 (ptp-110)
REVERT: B  152 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8100 (tppt)
REVERT: B  367 MET cc_start: 0.8753 (mmm) cc_final: 0.8426 (mmt)
REVERT: C   51 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8087 (tm-30)
REVERT: C   74 ARG cc_start: 0.7382 (mmt180) cc_final: 0.7117 (mtt-85)
REVERT: D   44 MET cc_start: 0.8956 (tpt) cc_final: 0.8166 (tpt)
REVERT: D  119 GLU cc_start: 0.8807 (tp30) cc_final: 0.8529 (tp30)
REVERT: D  139 LEU cc_start: 0.7804 (mt) cc_final: 0.7568 (mp)
REVERT: E   73 VAL cc_start: 0.8986 (t) cc_final: 0.8680 (p)
REVERT: F  119 MET cc_start: 0.4538 (OUTLIER) cc_final: 0.4288 (tpp)
REVERT: F  276 MET cc_start: 0.7964 (mtt) cc_final: 0.7415 (mtp)
REVERT: F  285 MET cc_start: 0.6369 (tmm) cc_final: 0.5981 (tmm)
REVERT: F  319 TYR cc_start: 0.7369 (m-10) cc_final: 0.7042 (m-10)
  outliers start: 20
  outliers final: 13
  residues processed: 184
  average time/residue: 0.1182
  time to fit residues: 32.9517
Evaluate side-chains
  166 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain C residue  110 GLN
Chi-restraints excluded: chain D residue   66 ILE
Chi-restraints excluded: chain D residue  124 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue  119 MET
Chi-restraints excluded: chain F residue  150 LEU
Chi-restraints excluded: chain F residue  356 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 144 optimal weight:    0.0370
   chunk 103 optimal weight:   10.0000
   chunk 64 optimal weight:    1.9990
   chunk 118 optimal weight:    7.9990
   chunk 60 optimal weight:    0.6980
   chunk 174 optimal weight:    9.9990
   chunk 105 optimal weight:    2.9990
   chunk 113 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 99 optimal weight:    0.0170
   overall best weight:    0.5296

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

Flipped N/Q/H residues before XYZ refinement:
B 243 GLN
D  68 ASN
F 216 ASN
F 244 GLN
** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.167298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.115306 restraints weight = 18795.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 2.43
r_work: 0.3178 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  15038  Z= 0.105
  Angle     :  0.527  11.119  20422  Z= 0.275
  Chirality :  0.041   0.165   2306
  Planarity :  0.005   0.072   2567
  Dihedral  :  7.865  77.790   2151
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 11.86 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.19), residues: 1880
  helix:  0.99 (0.18), residues: 836
  sheet: -2.52 (0.37), residues: 146
  loop : -1.82 (0.19), residues: 898

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 118 
 TYR   0.013   0.001   TYR D 141 
 PHE   0.027   0.001   PHE F 182 
 TRP   0.024   0.001   TRP B 103 
 HIS   0.005   0.001   HIS F 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (15035)
  covalent geometry    : angle       0.52576 (20418)
  hydrogen bonds       : bond        0.04025 (  671)
  hydrogen bonds       : angle       4.54350 ( 1938)
  metal coordination   : bond        0.00104 (    3)
  metal coordination   : angle       3.10397 (    4)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 178
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A    5 LYS cc_start: 0.8851 (mttp) cc_final: 0.8273 (mttm)
REVERT: B  151 ARG cc_start: 0.5677 (mmm160) cc_final: 0.4822 (ptp-110)
REVERT: B  152 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8282 (tppt)
REVERT: C   51 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8212 (tm-30)
REVERT: C   74 ARG cc_start: 0.7482 (mmt180) cc_final: 0.7154 (mtt-85)
REVERT: C  141 HIS cc_start: 0.8676 (p90) cc_final: 0.8439 (p-80)
REVERT: D   18 ASN cc_start: 0.8457 (t0) cc_final: 0.7981 (t0)
REVERT: D  119 GLU cc_start: 0.8831 (tp30) cc_final: 0.8602 (tp30)
REVERT: D  139 LEU cc_start: 0.8018 (mt) cc_final: 0.7810 (mp)
REVERT: E   17 MET cc_start: 0.8271 (mmm) cc_final: 0.8013 (mmt)
REVERT: F  119 MET cc_start: 0.4719 (OUTLIER) cc_final: 0.4429 (tpp)
REVERT: F  276 MET cc_start: 0.8070 (mtt) cc_final: 0.7780 (mtp)
REVERT: F  285 MET cc_start: 0.6315 (tmm) cc_final: 0.5985 (tmm)
REVERT: F  289 ARG cc_start: 0.5850 (ttt-90) cc_final: 0.5633 (ptm-80)
REVERT: F  293 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7395 (m-80)
REVERT: F  319 TYR cc_start: 0.7295 (m-10) cc_final: 0.7088 (m-80)
REVERT: F  336 HIS cc_start: 0.7955 (m-70) cc_final: 0.7521 (m-70)
  outliers start: 21
  outliers final: 12
  residues processed: 193
  average time/residue: 0.1164
  time to fit residues: 34.0419
Evaluate side-chains
  175 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 161
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain D residue   66 ILE
Chi-restraints excluded: chain D residue  124 LYS
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue  119 MET
Chi-restraints excluded: chain F residue  214 MET
Chi-restraints excluded: chain F residue  293 PHE
Chi-restraints excluded: chain F residue  356 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 141 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 167 optimal weight:   20.0000
   chunk 39 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 172 optimal weight:   10.0000
   chunk 56 optimal weight:    0.0870
   chunk 65 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 104 optimal weight:    4.9990
   overall best weight:    1.7562

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

Flipped N/Q/H residues before XYZ refinement:
A 242 GLN
B 243 GLN
D  68 ASN
** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.161602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.108470 restraints weight = 18783.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.73
r_work: 0.3105 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15038  Z= 0.169
  Angle     :  0.557  11.854  20422  Z= 0.289
  Chirality :  0.043   0.151   2306
  Planarity :  0.005   0.068   2567
  Dihedral  :  7.680  73.685   2151
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.03 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.74 (0.19), residues: 1880
  helix:  1.04 (0.18), residues: 845
  sheet: -2.48 (0.35), residues: 163
  loop : -1.65 (0.20), residues: 872

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 104 
 TYR   0.017   0.001   TYR B 360 
 PHE   0.023   0.001   PHE D  50 
 TRP   0.027   0.002   TRP F 250 
 HIS   0.004   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (15035)
  covalent geometry    : angle       0.55477 (20418)
  hydrogen bonds       : bond        0.04564 (  671)
  hydrogen bonds       : angle       4.51029 ( 1938)
  metal coordination   : bond        0.01167 (    3)
  metal coordination   : angle       3.28916 (    4)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 167
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.8764 (mttp) cc_final: 0.8124 (mttm)
REVERT: B   42 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7817 (mtmm)
REVERT: B  151 ARG cc_start: 0.5553 (mmm160) cc_final: 0.4451 (ptp-110)
REVERT: B  152 LYS cc_start: 0.8888 (ttmt) cc_final: 0.8058 (tppt)
REVERT: C   51 GLN cc_start: 0.8380 (tm-30) cc_final: 0.8105 (tm-30)
REVERT: D   18 ASN cc_start: 0.8346 (t0) cc_final: 0.7836 (t0)
REVERT: D  119 GLU cc_start: 0.8794 (tp30) cc_final: 0.8503 (tp30)
REVERT: D  139 LEU cc_start: 0.7758 (mt) cc_final: 0.7523 (mp)
REVERT: E   15 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8069 (mp0)
REVERT: E   17 MET cc_start: 0.8263 (mmm) cc_final: 0.7975 (mmt)
REVERT: E   51 ILE cc_start: 0.8298 (mm) cc_final: 0.7870 (tp)
REVERT: F  119 MET cc_start: 0.4513 (OUTLIER) cc_final: 0.4229 (tpp)
REVERT: F  123 LEU cc_start: 0.4311 (OUTLIER) cc_final: 0.4020 (tt)
REVERT: F  285 MET cc_start: 0.6269 (tmm) cc_final: 0.5905 (tmm)
REVERT: F  293 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7429 (m-80)
REVERT: F  319 TYR cc_start: 0.7199 (m-10) cc_final: 0.6857 (m-80)
  outliers start: 37
  outliers final: 21
  residues processed: 193
  average time/residue: 0.1173
  time to fit residues: 34.3717
Evaluate side-chains
  180 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain D residue   66 ILE
Chi-restraints excluded: chain D residue  124 LYS
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  105 LEU
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  119 MET
Chi-restraints excluded: chain F residue  123 LEU
Chi-restraints excluded: chain F residue  181 ASP
Chi-restraints excluded: chain F residue  200 TYR
Chi-restraints excluded: chain F residue  228 VAL
Chi-restraints excluded: chain F residue  293 PHE
Chi-restraints excluded: chain F residue  356 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 91 optimal weight:    8.9990
   chunk 168 optimal weight:   20.0000
   chunk 51 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   chunk 151 optimal weight:   30.0000
   chunk 5 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 135 optimal weight:    0.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
B 243 GLN
D  68 ASN
F 336 HIS
** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.163747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.110296 restraints weight = 18609.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.83
r_work: 0.3126 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15038  Z= 0.140
  Angle     :  0.534  11.626  20422  Z= 0.276
  Chirality :  0.042   0.161   2306
  Planarity :  0.005   0.063   2567
  Dihedral  :  7.511  72.357   2151
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.87 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.19), residues: 1880
  helix:  1.22 (0.18), residues: 846
  sheet: -2.39 (0.35), residues: 171
  loop : -1.57 (0.20), residues: 863

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 118 
 TYR   0.015   0.001   TYR B 360 
 PHE   0.030   0.001   PHE F 182 
 TRP   0.030   0.002   TRP F 250 
 HIS   0.003   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (15035)
  covalent geometry    : angle       0.53216 (20418)
  hydrogen bonds       : bond        0.04256 (  671)
  hydrogen bonds       : angle       4.41680 ( 1938)
  metal coordination   : bond        0.00916 (    3)
  metal coordination   : angle       3.36229 (    4)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 163
  time to evaluate  : 0.576 
Fit side-chains
REVERT: A    5 LYS cc_start: 0.8795 (mttp) cc_final: 0.8172 (mttm)
REVERT: B  151 ARG cc_start: 0.5558 (mmm160) cc_final: 0.4532 (ptp-110)
REVERT: B  152 LYS cc_start: 0.8924 (ttmt) cc_final: 0.8135 (tppt)
REVERT: C   51 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: D   18 ASN cc_start: 0.8389 (t0) cc_final: 0.7882 (t0)
REVERT: D  119 GLU cc_start: 0.8810 (tp30) cc_final: 0.8524 (tp30)
REVERT: D  139 LEU cc_start: 0.7808 (mt) cc_final: 0.7589 (mp)
REVERT: E    1 MET cc_start: 0.6160 (mmt) cc_final: 0.5226 (ptm)
REVERT: E   17 MET cc_start: 0.8273 (mmm) cc_final: 0.8023 (mmt)
REVERT: E   51 ILE cc_start: 0.8401 (mm) cc_final: 0.8022 (tp)
REVERT: F  123 LEU cc_start: 0.4268 (OUTLIER) cc_final: 0.3970 (tt)
REVERT: F  214 MET cc_start: 0.5922 (OUTLIER) cc_final: 0.5643 (mpp)
REVERT: F  285 MET cc_start: 0.6138 (tmm) cc_final: 0.5791 (tmm)
REVERT: F  293 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7421 (m-80)
REVERT: F  319 TYR cc_start: 0.7135 (m-10) cc_final: 0.6827 (m-80)
  outliers start: 37
  outliers final: 21
  residues processed: 190
  average time/residue: 0.1104
  time to fit residues: 32.6536
Evaluate side-chains
  179 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 155
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain D residue   66 ILE
Chi-restraints excluded: chain D residue  124 LYS
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  105 LEU
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   98 ILE
Chi-restraints excluded: chain F residue  123 LEU
Chi-restraints excluded: chain F residue  214 MET
Chi-restraints excluded: chain F residue  249 ILE
Chi-restraints excluded: chain F residue  293 PHE
Chi-restraints excluded: chain F residue  356 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 149 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   chunk 3 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 142 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 124 optimal weight:    2.9990
   chunk 174 optimal weight:    8.9990
   chunk 103 optimal weight:    9.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 242 GLN
B 243 GLN
D  68 ASN
** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.158691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.105161 restraints weight = 18941.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.69
r_work: 0.3061 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051  15038  Z= 0.279
  Angle     :  0.644  12.109  20422  Z= 0.330
  Chirality :  0.046   0.155   2306
  Planarity :  0.005   0.063   2567
  Dihedral  :  7.754  69.159   2151
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.58 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.19), residues: 1880
  helix:  0.86 (0.18), residues: 846
  sheet: -2.42 (0.38), residues: 155
  loop : -1.57 (0.20), residues: 879

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 118 
 TYR   0.021   0.002   TYR B 360 
 PHE   0.036   0.002   PHE F 182 
 TRP   0.030   0.002   TRP F 250 
 HIS   0.006   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00691 (15035)
  covalent geometry    : angle       0.64022 (20418)
  hydrogen bonds       : bond        0.05373 (  671)
  hydrogen bonds       : angle       4.63030 ( 1938)
  metal coordination   : bond        0.02255 (    3)
  metal coordination   : angle       5.01341 (    4)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 158
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.8727 (mttp) cc_final: 0.8185 (mttm)
REVERT: B   42 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7848 (mtmm)
REVERT: B  151 ARG cc_start: 0.5660 (mmm160) cc_final: 0.4481 (ptp-110)
REVERT: B  152 LYS cc_start: 0.8882 (ttmt) cc_final: 0.8062 (tppt)
REVERT: C   51 GLN cc_start: 0.8322 (tm-30) cc_final: 0.8039 (tm-30)
REVERT: C   74 ARG cc_start: 0.7342 (mmt180) cc_final: 0.7038 (mtt-85)
REVERT: D  119 GLU cc_start: 0.8781 (tp30) cc_final: 0.8465 (tp30)
REVERT: E    1 MET cc_start: 0.6246 (mmt) cc_final: 0.5400 (ptm)
REVERT: E   17 MET cc_start: 0.8310 (mmm) cc_final: 0.8027 (mmt)
REVERT: F  123 LEU cc_start: 0.4209 (OUTLIER) cc_final: 0.3912 (tt)
REVERT: F  214 MET cc_start: 0.6045 (OUTLIER) cc_final: 0.5711 (mpp)
REVERT: F  285 MET cc_start: 0.6112 (tmm) cc_final: 0.5791 (tmm)
REVERT: F  293 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7428 (m-80)
REVERT: F  319 TYR cc_start: 0.7176 (m-10) cc_final: 0.6901 (m-80)
REVERT: F  394 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8181 (tp)
  outliers start: 38
  outliers final: 25
  residues processed: 189
  average time/residue: 0.1110
  time to fit residues: 32.1275
Evaluate side-chains
  185 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 156
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain D residue   66 ILE
Chi-restraints excluded: chain D residue  124 LYS
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   98 ILE
Chi-restraints excluded: chain F residue  123 LEU
Chi-restraints excluded: chain F residue  181 ASP
Chi-restraints excluded: chain F residue  209 ILE
Chi-restraints excluded: chain F residue  214 MET
Chi-restraints excluded: chain F residue  249 ILE
Chi-restraints excluded: chain F residue  293 PHE
Chi-restraints excluded: chain F residue  356 HIS
Chi-restraints excluded: chain F residue  390 MET
Chi-restraints excluded: chain F residue  394 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 171 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   chunk 138 optimal weight:    0.1980
   chunk 173 optimal weight:    9.9990
   chunk 166 optimal weight:   20.0000
   chunk 112 optimal weight:    1.9990
   chunk 71 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:
B 243 GLN
C 110 GLN
D  68 ASN
F 384 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.166193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.113962 restraints weight = 18578.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 2.79
r_work: 0.3159 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3031 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  15038  Z= 0.107
  Angle     :  0.517  11.332  20422  Z= 0.267
  Chirality :  0.041   0.147   2306
  Planarity :  0.004   0.062   2567
  Dihedral  :  7.357  71.099   2151
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.01 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.20), residues: 1880
  helix:  1.41 (0.18), residues: 841
  sheet: -2.22 (0.38), residues: 157
  loop : -1.48 (0.20), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 408 
 TYR   0.013   0.001   TYR D 141 
 PHE   0.029   0.001   PHE F 182 
 TRP   0.036   0.002   TRP F 250 
 HIS   0.003   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (15035)
  covalent geometry    : angle       0.51553 (20418)
  hydrogen bonds       : bond        0.03903 (  671)
  hydrogen bonds       : angle       4.30239 ( 1938)
  metal coordination   : bond        0.00632 (    3)
  metal coordination   : angle       2.91768 (    4)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 167
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.8877 (mttp) cc_final: 0.8305 (mttm)
REVERT: B  151 ARG cc_start: 0.5661 (mmm160) cc_final: 0.4774 (ptp-110)
REVERT: B  152 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8281 (tppt)
REVERT: C   51 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8184 (tm-30)
REVERT: C   74 ARG cc_start: 0.7421 (mmt180) cc_final: 0.7094 (mtt-85)
REVERT: C  141 HIS cc_start: 0.8678 (p90) cc_final: 0.8445 (p-80)
REVERT: D   18 ASN cc_start: 0.8497 (t0) cc_final: 0.8042 (t0)
REVERT: D  119 GLU cc_start: 0.8809 (tp30) cc_final: 0.8568 (tp30)
REVERT: D  139 LEU cc_start: 0.8048 (mt) cc_final: 0.7818 (mp)
REVERT: E    1 MET cc_start: 0.6250 (mmt) cc_final: 0.5382 (ptm)
REVERT: E   51 ILE cc_start: 0.8584 (mm) cc_final: 0.8283 (tp)
REVERT: F  123 LEU cc_start: 0.4210 (OUTLIER) cc_final: 0.3979 (tp)
REVERT: F  214 MET cc_start: 0.5711 (mpp) cc_final: 0.5490 (mpp)
REVERT: F  285 MET cc_start: 0.6040 (tmm) cc_final: 0.5779 (tmm)
REVERT: F  293 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7386 (m-80)
REVERT: F  308 TRP cc_start: 0.7785 (m100) cc_final: 0.7469 (m100)
REVERT: F  319 TYR cc_start: 0.7123 (m-10) cc_final: 0.6858 (m-80)
  outliers start: 26
  outliers final: 20
  residues processed: 187
  average time/residue: 0.1079
  time to fit residues: 31.2003
Evaluate side-chains
  179 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain D residue   66 ILE
Chi-restraints excluded: chain D residue  124 LYS
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   98 ILE
Chi-restraints excluded: chain F residue  123 LEU
Chi-restraints excluded: chain F residue  181 ASP
Chi-restraints excluded: chain F residue  209 ILE
Chi-restraints excluded: chain F residue  293 PHE
Chi-restraints excluded: chain F residue  356 HIS
Chi-restraints excluded: chain F residue  390 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 163 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 132 optimal weight:    4.9990
   chunk 111 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 133 optimal weight:    0.5980
   chunk 169 optimal weight:    6.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
B 243 GLN
D  68 ASN
E 107 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.164156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.111468 restraints weight = 18805.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 2.74
r_work: 0.3138 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15038  Z= 0.149
  Angle     :  0.550  13.464  20422  Z= 0.279
  Chirality :  0.042   0.150   2306
  Planarity :  0.004   0.060   2567
  Dihedral  :  7.311  69.619   2151
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 16.33 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.19), residues: 1880
  helix:  1.38 (0.18), residues: 845
  sheet: -2.17 (0.38), residues: 164
  loop : -1.42 (0.20), residues: 871

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 408 
 TYR   0.015   0.001   TYR B 360 
 PHE   0.037   0.001   PHE F 182 
 TRP   0.029   0.002   TRP F 250 
 HIS   0.004   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (15035)
  covalent geometry    : angle       0.54788 (20418)
  hydrogen bonds       : bond        0.04282 (  671)
  hydrogen bonds       : angle       4.30985 ( 1938)
  metal coordination   : bond        0.01092 (    3)
  metal coordination   : angle       3.18705 (    4)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 166
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.8875 (mttp) cc_final: 0.8224 (mttm)
REVERT: A   39 MET cc_start: 0.8863 (tmm) cc_final: 0.8600 (ttp)
REVERT: B  151 ARG cc_start: 0.5607 (mmm160) cc_final: 0.4564 (ptp-110)
REVERT: B  152 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8185 (tppt)
REVERT: C   51 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8155 (tm-30)
REVERT: C   74 ARG cc_start: 0.7300 (mmt180) cc_final: 0.6964 (mtt-85)
REVERT: D   18 ASN cc_start: 0.8419 (t0) cc_final: 0.7921 (t0)
REVERT: D  119 GLU cc_start: 0.8797 (tp30) cc_final: 0.8511 (tp30)
REVERT: D  139 LEU cc_start: 0.7911 (mt) cc_final: 0.7676 (mp)
REVERT: D  146 MET cc_start: 0.7636 (mmt) cc_final: 0.7213 (mmt)
REVERT: E    1 MET cc_start: 0.6251 (mmt) cc_final: 0.5311 (ptm)
REVERT: E   17 MET cc_start: 0.8391 (tpp) cc_final: 0.8092 (mmt)
REVERT: E   51 ILE cc_start: 0.8511 (mm) cc_final: 0.8132 (tp)
REVERT: F  123 LEU cc_start: 0.4094 (OUTLIER) cc_final: 0.3885 (tp)
REVERT: F  214 MET cc_start: 0.5685 (mpp) cc_final: 0.5436 (mpp)
REVERT: F  285 MET cc_start: 0.6122 (tmm) cc_final: 0.5864 (tmm)
REVERT: F  293 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7421 (m-80)
REVERT: F  319 TYR cc_start: 0.7083 (m-10) cc_final: 0.6808 (m-80)
  outliers start: 27
  outliers final: 20
  residues processed: 186
  average time/residue: 0.1044
  time to fit residues: 30.3207
Evaluate side-chains
  183 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain D residue   66 ILE
Chi-restraints excluded: chain D residue  124 LYS
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   98 ILE
Chi-restraints excluded: chain F residue  123 LEU
Chi-restraints excluded: chain F residue  209 ILE
Chi-restraints excluded: chain F residue  293 PHE
Chi-restraints excluded: chain F residue  356 HIS
Chi-restraints excluded: chain F residue  390 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0270
   chunk 115 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 111 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 152 optimal weight:   40.0000
   chunk 57 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 151 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.7040

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

Flipped N/Q/H residues before XYZ refinement:
A 209 HIS
B 243 GLN
D  68 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.166994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.114671 restraints weight = 18720.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.85
r_work: 0.3180 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  15038  Z= 0.105
  Angle     :  0.513  12.647  20422  Z= 0.262
  Chirality :  0.041   0.161   2306
  Planarity :  0.004   0.060   2567
  Dihedral  :  7.120  70.401   2151
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.66 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.20), residues: 1880
  helix:  1.64 (0.19), residues: 841
  sheet: -2.03 (0.39), residues: 156
  loop : -1.37 (0.20), residues: 883

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 408 
 TYR   0.013   0.001   TYR D 141 
 PHE   0.026   0.001   PHE F 182 
 TRP   0.045   0.002   TRP F 308 
 HIS   0.003   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (15035)
  covalent geometry    : angle       0.51185 (20418)
  hydrogen bonds       : bond        0.03714 (  671)
  hydrogen bonds       : angle       4.16858 ( 1938)
  metal coordination   : bond        0.00577 (    3)
  metal coordination   : angle       2.59215 (    4)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 171
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.8879 (mttp) cc_final: 0.8233 (mttm)
REVERT: A   39 MET cc_start: 0.8781 (tmm) cc_final: 0.8494 (ttp)
REVERT: B  151 ARG cc_start: 0.5562 (mmm160) cc_final: 0.4569 (ptp-110)
REVERT: B  152 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8212 (tppt)
REVERT: C   51 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8166 (tm-30)
REVERT: C   74 ARG cc_start: 0.7217 (mmt180) cc_final: 0.6876 (mtt-85)
REVERT: D   18 ASN cc_start: 0.8386 (t0) cc_final: 0.7878 (t0)
REVERT: D   50 PHE cc_start: 0.7747 (t80) cc_final: 0.6433 (m-80)
REVERT: D  119 GLU cc_start: 0.8784 (tp30) cc_final: 0.8519 (tp30)
REVERT: D  139 LEU cc_start: 0.7857 (mt) cc_final: 0.7653 (mp)
REVERT: D  146 MET cc_start: 0.7531 (mmt) cc_final: 0.7282 (mmt)
REVERT: E    1 MET cc_start: 0.6157 (mmt) cc_final: 0.5237 (ptm)
REVERT: E   51 ILE cc_start: 0.8521 (mm) cc_final: 0.8163 (tp)
REVERT: F  123 LEU cc_start: 0.4132 (OUTLIER) cc_final: 0.3912 (tp)
REVERT: F  214 MET cc_start: 0.5403 (mpp) cc_final: 0.5029 (mpp)
REVERT: F  293 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7430 (m-80)
REVERT: F  319 TYR cc_start: 0.6972 (m-10) cc_final: 0.6683 (m-80)
  outliers start: 26
  outliers final: 22
  residues processed: 191
  average time/residue: 0.1198
  time to fit residues: 34.4199
Evaluate side-chains
  186 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain D residue   66 ILE
Chi-restraints excluded: chain D residue  124 LYS
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   98 ILE
Chi-restraints excluded: chain F residue  123 LEU
Chi-restraints excluded: chain F residue  181 ASP
Chi-restraints excluded: chain F residue  209 ILE
Chi-restraints excluded: chain F residue  293 PHE
Chi-restraints excluded: chain F residue  356 HIS
Chi-restraints excluded: chain F residue  390 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 15 optimal weight:    0.5980
   chunk 60 optimal weight:    0.0040
   chunk 110 optimal weight:    3.9990
   chunk 112 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 131 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 137 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 121 optimal weight:    0.7980
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
B 243 GLN
C 141 HIS
D  68 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.167811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.115436 restraints weight = 18607.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.90
r_work: 0.3191 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  15038  Z= 0.101
  Angle     :  0.517  12.746  20422  Z= 0.261
  Chirality :  0.041   0.146   2306
  Planarity :  0.004   0.062   2567
  Dihedral  :  6.970  69.831   2151
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 17.17 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.20), residues: 1880
  helix:  1.73 (0.19), residues: 841
  sheet: -1.90 (0.39), residues: 157
  loop : -1.30 (0.20), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 408 
 TYR   0.013   0.001   TYR D 141 
 PHE   0.036   0.001   PHE F 182 
 TRP   0.036   0.002   TRP F 308 
 HIS   0.006   0.001   HIS C 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (15035)
  covalent geometry    : angle       0.51592 (20418)
  hydrogen bonds       : bond        0.03605 (  671)
  hydrogen bonds       : angle       4.10978 ( 1938)
  metal coordination   : bond        0.00431 (    3)
  metal coordination   : angle       2.43180 (    4)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 171
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.8876 (mttp) cc_final: 0.8234 (mttm)
REVERT: A   39 MET cc_start: 0.8769 (tmm) cc_final: 0.8487 (ttp)
REVERT: B  151 ARG cc_start: 0.5563 (mmm160) cc_final: 0.4576 (ptp-110)
REVERT: B  152 LYS cc_start: 0.8952 (ttmt) cc_final: 0.8209 (tppt)
REVERT: C   51 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8186 (tm-30)
REVERT: C   74 ARG cc_start: 0.7253 (mmt180) cc_final: 0.6907 (mtt-85)
REVERT: D   18 ASN cc_start: 0.8347 (t0) cc_final: 0.7830 (t0)
REVERT: D   50 PHE cc_start: 0.7774 (t80) cc_final: 0.6463 (m-80)
REVERT: D  112 CYS cc_start: 0.9261 (t) cc_final: 0.9007 (t)
REVERT: D  119 GLU cc_start: 0.8786 (tp30) cc_final: 0.8510 (tp30)
REVERT: E   51 ILE cc_start: 0.8529 (mm) cc_final: 0.8169 (tp)
REVERT: F  123 LEU cc_start: 0.3963 (OUTLIER) cc_final: 0.3749 (tp)
REVERT: F  214 MET cc_start: 0.5299 (mpp) cc_final: 0.4991 (mpp)
REVERT: F  293 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7404 (m-80)
REVERT: F  319 TYR cc_start: 0.6891 (m-10) cc_final: 0.6682 (m-80)
  outliers start: 22
  outliers final: 16
  residues processed: 187
  average time/residue: 0.1176
  time to fit residues: 33.4543
Evaluate side-chains
  184 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain D residue   66 ILE
Chi-restraints excluded: chain D residue  124 LYS
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   98 ILE
Chi-restraints excluded: chain F residue  123 LEU
Chi-restraints excluded: chain F residue  209 ILE
Chi-restraints excluded: chain F residue  293 PHE
Chi-restraints excluded: chain F residue  356 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 120 optimal weight:    4.9990
   chunk 160 optimal weight:   10.0000
   chunk 125 optimal weight:    0.0070
   chunk 93 optimal weight:    7.9990
   chunk 158 optimal weight:    6.9990
   chunk 89 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 142 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    3.6006

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

Flipped N/Q/H residues before XYZ refinement:
B 243 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.159108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.106176 restraints weight = 18719.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 2.95
r_work: 0.3058 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.057  15038  Z= 0.314
  Angle     :  0.685  12.463  20422  Z= 0.345
  Chirality :  0.047   0.160   2306
  Planarity :  0.005   0.061   2567
  Dihedral  :  7.469  67.540   2151
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 16.98 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.19), residues: 1880
  helix:  0.99 (0.18), residues: 847
  sheet: -2.14 (0.37), residues: 167
  loop : -1.42 (0.20), residues: 866

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 161 
 TYR   0.021   0.002   TYR B 360 
 PHE   0.032   0.002   PHE F 182 
 TRP   0.033   0.002   TRP F 308 
 HIS   0.007   0.001   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00776 (15035)
  covalent geometry    : angle       0.67944 (20418)
  hydrogen bonds       : bond        0.05584 (  671)
  hydrogen bonds       : angle       4.57369 ( 1938)
  metal coordination   : bond        0.02789 (    3)
  metal coordination   : angle       6.19356 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4546.78 seconds
wall clock time: 78 minutes 19.50 seconds (4699.50 seconds total)