Starting phenix.real_space_refine
on Wed Mar  4 18:47:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xk3_33242/03_2026/7xk3_33242.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xk3_33242/03_2026/7xk3_33242.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xk3_33242/03_2026/7xk3_33242.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xk3_33242/03_2026/7xk3_33242.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xk3_33242/03_2026/7xk3_33242.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xk3_33242/03_2026/7xk3_33242.map"
  }
  resolution = 3.1
  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=  -0.000 sd=   0.098
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    9617      2.51       5
     N    2412      2.21       5
     O    2714      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14846
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 3421
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 446, 3416
          Classifications: {'peptide': 446}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 422}
      Conformer: "B"
        Number of residues, atoms: 446, 3416
          Classifications: {'peptide': 446}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 422}
          bond proxies already assigned to first conformer: 3474
    Chain: "B"
      Number of atoms: 2964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 2964
          Classifications: {'peptide': 387}
          Link IDs: {'PTRANS': 14, 'TRANS': 372}
    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: 1562
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1562
          Classifications: {'peptide': 204}
          Link IDs: {'PTRANS': 9, 'TRANS': 194}
    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: 3165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 408, 3165
          Classifications: {'peptide': 408}
          Link IDs: {'PTRANS': 24, 'TRANS': 383}
    Chain: "B"
      Number of atoms: 194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 194
          Unusual residues: {'FMN': 1, 'LMT': 1, 'PEE': 2, 'RBF': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "C"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'FMN': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 39
          Unusual residues: {'FES': 1, 'LMT': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 57
          Unusual residues: {'FAD': 1, 'FES': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   9093  SG  CYS D 112      42.636  75.974  65.219  1.00 35.57           S
  ATOM  10059  SG  CYS E  26      44.816  71.966  66.205  1.00 30.51           S
  ATOM   8454  SG  CYS D  29      43.184  69.115  62.048  1.00 30.00           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AALA A 338 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BALA A 338 " occ=0.50
  Time building chain proxies: 3.41, per 1000 atoms: 0.23
  Number of scatterers: 14846
  At special positions: 0
  Unit cell: (88, 127.6, 153.12, 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    2714      8.00
     N    2412      7.00
     C    9617      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.46
  Conformation dependent library (CDL) restraints added in 797.7 milliseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" FES D 301 "
        pdb="FE2  FES D 301 " - pdb=" SG  CYS D  29 "
        pdb="FE1  FES D 301 " - pdb=" SG  CYS E  26 "
        pdb="FE1  FES D 301 " - pdb=" SG  CYS D 112 "
        pdb="FE2  FES D 301 " - pdb=" SG  CYS E 120 "
      pdb=" FES F 501 "
        pdb="FE1  FES F 501 " - pdb=" SG  CYS F 111 "
        pdb="FE2  FES F 501 " - pdb=" SG  CYS F  76 "
        pdb="FE2  FES F 501 " - pdb=" SG  CYS F  70 "
        pdb="FE1  FES F 501 " - pdb=" SG  CYS F  79 "
      Number of angles added : 12


  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3422

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 16 sheets defined
      50.3% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 36
      removed outlier: 3.839A  pdb=" N   TYR A  36 " --> pdb=" O   GLY A  33 " (cutoff:3.500A)
    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: 3.577A  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
      removed outlier: 3.684A  pdb=" N   HIS A 223 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
    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
    Processing helix  chain 'A' and resid 351 through 355
      removed outlier: 4.137A  pdb=" N   HIS A 354 " --> pdb=" O   PHE A 351 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU A 355 " --> pdb=" O   LEU A 352 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 351 through 355'
    Processing helix  chain 'A' and resid 389 through 399
    Processing helix  chain 'A' and resid 401 through 409
      removed outlier: 3.703A  pdb=" N   ALA A 405 " --> pdb=" O   ASP A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 413
      removed outlier: 3.748A  pdb=" N   LEU A 413 " --> pdb=" O   ALA A 410 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 410 through 413'
    Processing helix  chain 'A' and resid 414 through 417
    Processing helix  chain 'A' and resid 418 through 424
    Processing helix  chain 'A' and resid 430 through 445
      removed outlier: 3.910A  pdb=" N   LEU A 434 " --> pdb=" O   GLU A 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 35
      removed outlier: 4.105A  pdb=" N   PHE B  34 " --> pdb=" O   ALA B  30 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   TYR B  35 " --> pdb=" O   ALA B  31 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 30 through 35'
    Processing helix  chain 'B' and resid 52 through 62
    Processing helix  chain 'B' and resid 64 through 87
    Processing helix  chain 'B' and resid 89 through 97
      removed outlier: 4.071A  pdb=" N   ALA B  93 " --> pdb=" O   GLY B  89 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ALA B  94 " --> pdb=" O   ASP B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 109
    Processing helix  chain 'B' and resid 117 through 151
      removed outlier: 3.620A  pdb=" N   LYS B 121 " --> pdb=" O   GLY B 117 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU B 124 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   TYR B 128 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
      Proline residue:  B 131  - end of helix
      removed outlier: 3.641A  pdb=" N   TRP B 143 " --> pdb=" O   VAL B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 169
      removed outlier: 3.885A  pdb=" N   THR B 162 " --> pdb=" O   GLY B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 189
    Processing helix  chain 'B' and resid 203 through 216
    Processing helix  chain 'B' and resid 240 through 245
    Processing helix  chain 'B' and resid 246 through 248
      No H-bonds generated for 'chain 'B' and resid 246 through 248'
    Processing helix  chain 'B' and resid 259 through 266
    Processing helix  chain 'B' and resid 276 through 290
    Processing helix  chain 'B' and resid 294 through 316
    Processing helix  chain 'B' and resid 320 through 325
      removed outlier: 3.815A  pdb=" N   PHE B 323 " --> pdb=" O   ASN B 320 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASN B 324 " --> pdb=" O   ALA B 321 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   MET B 325 " --> pdb=" O   MET B 322 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 320 through 325'
    Processing helix  chain 'B' and resid 326 through 331
      removed outlier: 3.696A  pdb=" N   LEU B 331 " --> pdb=" O   TRP B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 343
      removed outlier: 3.656A  pdb=" N   GLY B 339 " --> pdb=" O   GLY B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 375
      removed outlier: 4.000A  pdb=" N   TRP B 358 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ALA B 359 " --> pdb=" O   SER B 355 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ASN B 375 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 410
      removed outlier: 4.001A  pdb=" N   LEU B 391 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   PHE B 392 " --> pdb=" O   PHE B 388 " (cutoff:3.500A)
      Proline residue:  B 394  - end of helix
      removed outlier: 3.528A  pdb=" N   ARG B 407 " --> pdb=" O   ARG B 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 32
      removed outlier: 3.524A  pdb=" N   VAL C  31 " --> pdb=" O   SER C  27 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 54
      removed outlier: 3.857A  pdb=" N   ASP C  44 " --> pdb=" O   ASN C  40 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   LYS C  45 " --> pdb=" O   ALA C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 70
    Processing helix  chain 'C' and resid 92 through 99
    Processing helix  chain 'C' and resid 178 through 181
      removed outlier: 3.796A  pdb=" N   GLU C 181 " --> pdb=" O   GLY C 178 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 178 through 181'
    Processing helix  chain 'C' and resid 182 through 187
    Processing helix  chain 'C' and resid 224 through 239
      removed outlier: 3.755A  pdb=" N   SER C 228 " --> pdb=" O   ALA C 224 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   GLY C 230 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 254
    Processing helix  chain 'D' and resid 8 through 17
      Proline residue:  D  14  - end of helix
    Processing helix  chain 'D' and resid 28 through 34
    Processing helix  chain 'D' and resid 37 through 62
    Processing helix  chain 'D' and resid 70 through 94
      removed outlier: 3.785A  pdb=" N   ALA D  92 " --> pdb=" O   GLN D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 101
      removed outlier: 3.829A  pdb=" N   GLN D 100 " --> pdb=" O   ASP D  96 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 107
      removed outlier: 4.211A  pdb=" N   GLY D 106 " --> pdb=" O   SER D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 120
      removed outlier: 3.814A  pdb=" N   MET D 115 " --> pdb=" O   ASN D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 125
      removed outlier: 3.712A  pdb=" N   SER D 125 " --> pdb=" O   ALA D 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 157
      removed outlier: 3.589A  pdb=" N   SER D 157 " --> pdb=" O   GLU D 153 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 179 through 183
    Processing helix  chain 'D' and resid 184 through 202
      removed outlier: 4.145A  pdb=" N   PHE D 188 " --> pdb=" O   ALA D 184 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE D 201 " --> pdb=" O   ALA D 197 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 14
      removed outlier: 3.642A  pdb=" N   LEU E   7 " --> pdb=" O   HIS E   3 " (cutoff:3.500A)
    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 75 through 77
      No H-bonds generated for 'chain 'E' and resid 75 through 77'
    Processing helix  chain 'E' and resid 78 through 102
    Processing helix  chain 'E' and resid 102 through 109
    Processing helix  chain 'E' and resid 119 through 133
    Processing helix  chain 'E' and resid 135 through 164
    Processing helix  chain 'E' and resid 165 through 167
      No H-bonds generated for 'chain 'E' and resid 165 through 167'
    Processing helix  chain 'E' and resid 175 through 191
      removed outlier: 3.666A  pdb=" N   THR E 179 " --> pdb=" O   GLY E 175 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 192 through 194
      No H-bonds generated for 'chain 'E' and resid 192 through 194'
    Processing helix  chain 'F' and resid 3 through 28
    Processing helix  chain 'F' and resid 54 through 63
    Processing helix  chain 'F' and resid 91 through 98
      removed outlier: 3.974A  pdb=" N   HIS F  97 " --> pdb=" O   THR F  93 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 99 through 104
    Processing helix  chain 'F' and resid 124 through 128
      removed outlier: 3.840A  pdb=" N   ILE F 127 " --> pdb=" O   PRO F 124 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   PHE F 128 " --> pdb=" O   GLU F 125 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 124 through 128'
    Processing helix  chain 'F' and resid 154 through 158
      removed outlier: 3.508A  pdb=" N   GLU F 158 " --> pdb=" O   PRO F 155 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 188 through 196
      removed outlier: 4.071A  pdb=" N   TRP F 192 " --> pdb=" O   TYR F 188 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 197 through 200
    Processing helix  chain 'F' and resid 243 through 252
    Processing helix  chain 'F' and resid 284 through 298
      removed outlier: 3.869A  pdb=" N   MET F 288 " --> pdb=" O   GLY F 284 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 319 through 330
    Processing helix  chain 'F' and resid 354 through 363
    Processing helix  chain 'F' and resid 380 through 395
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3
      removed outlier: 6.632A  pdb=" N   ILE A   2 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ALA A 148 " --> pdb=" O   TRP A 237 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   ILE A 239 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   PHE A 150 " --> pdb=" O   ILE A 239 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22
      removed outlier: 3.568A  pdb=" N   VAL A 325 " --> pdb=" O   ALA A 265 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   GLN A 322 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31
      removed outlier: 3.615A  pdb=" N   LEU A  31 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ASN A  80 " --> pdb=" O   GLN A  88 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   VAL A  90 " --> pdb=" O   GLU A  78 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   GLU A  78 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ILE A  92 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   VAL A  76 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   VAL A  94 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   GLY A  74 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43
      removed outlier: 3.508A  pdb=" N   PHE A  58 " --> pdb=" O   PHE A  68 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 366 through 367
      removed outlier: 4.826A  pdb=" N   LEU B  39 " --> pdb=" O   THR A 367 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 82 through 83
      removed outlier: 3.543A  pdb=" N   ASP C  82 " --> pdb=" O   ASP C  77 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   LYS C 132 " --> pdb=" O   ASP C 129 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 104
    Processing sheet with id=AA8, first strand: chain 'C' and resid 135 through 143
      removed outlier: 6.310A  pdb=" N   MET C 148 " --> pdb=" O   GLU C 169 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   GLU C 169 " --> pdb=" O   MET C 148 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   TYR C 150 " --> pdb=" O   TYR C 167 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   TYR C 167 " --> pdb=" O   TYR C 150 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   PHE C 152 " --> pdb=" O   LEU C 165 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   LEU C 165 " --> pdb=" O   PHE C 152 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ALA C 154 " --> pdb=" O   SER C 163 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 204 through 206
    Processing sheet with id=AB1, first strand: chain 'D' and resid 159 through 160
    Processing sheet with id=AB2, first strand: chain 'F' and resid 35 through 38
    Processing sheet with id=AB3, first strand: chain 'F' and resid 107 through 109
      removed outlier: 6.996A  pdb=" N   ASP F 120 " --> pdb=" O   LYS F  84 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 224 through 225
    Processing sheet with id=AB5, first strand: chain 'F' and resid 224 through 225
      removed outlier: 7.581A  pdb=" N   ILE F 147 " --> pdb=" O   ASN F 142 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   ASN F 142 " --> pdb=" O   ILE F 147 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   GLU F 149 " --> pdb=" O   ASN F 140 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   ASN F 140 " --> pdb=" O   GLU F 149 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   LYS F 151 " --> pdb=" O   ILE F 138 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 167 through 172
      removed outlier: 3.595A  pdb=" N   ARG F 210 " --> pdb=" O   ILE F 170 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 351 through 352
      removed outlier: 4.337A  pdb=" N   TYR F 351 " --> pdb=" O   CYS F 337 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU F 339 " --> pdb=" O   TYR F 351 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   MET F 305 " --> pdb=" O   VAL F 334 " (cutoff:3.500A)
      removed outlier: 8.473A  pdb=" N   HIS F 336 " --> pdb=" O   MET F 305 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   TYR F 307 " --> pdb=" O   HIS F 336 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   ALA F 338 " --> pdb=" O   TYR F 307 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   TYR F 309 " --> pdb=" O   ALA F 338 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   TYR F 375 " --> pdb=" O   LEU F 402 " (cutoff:3.500A)

    688 hydrogen bonds defined for protein.
    2001 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.35

  Time building geometry restraints manager: 1.86 seconds

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

  Histogram of bond lengths:
        1.16 -     1.37: 4769
        1.37 -     1.57: 10245
        1.57 -     1.78: 13
        1.78 -     1.99: 150
        1.99 -     2.20: 8
  Bond restraints: 15185
  Sorted by residual:
  bond pdb=" C4A RBF B 502 "
       pdb=" N5  RBF B 502 "
    ideal  model  delta    sigma   weight residual
    1.288  1.449 -0.161 2.00e-02 2.50e+03 6.51e+01
  bond pdb=" CA  SER B 239 "
       pdb=" CB  SER B 239 "
    ideal  model  delta    sigma   weight residual
    1.534  1.417  0.116 1.45e-02 4.76e+03 6.44e+01
  bond pdb=" C10 RBF B 502 "
       pdb=" N1  RBF B 502 "
    ideal  model  delta    sigma   weight residual
    1.304  1.463 -0.159 2.00e-02 2.50e+03 6.30e+01
  bond pdb=" CA  SER C 228 "
       pdb=" CB  SER C 228 "
    ideal  model  delta    sigma   weight residual
    1.529  1.420  0.109 1.55e-02 4.16e+03 4.92e+01
  bond pdb=" C5A RBF B 502 "
       pdb=" N5  RBF B 502 "
    ideal  model  delta    sigma   weight residual
    1.350  1.490 -0.140 2.00e-02 2.50e+03 4.89e+01
  ... (remaining 15180 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.33: 20234
        3.33 -     6.66: 300
        6.66 -     9.99: 30
        9.99 -    13.32: 12
       13.32 -    16.65: 6
  Bond angle restraints: 20582
  Sorted by residual:
  angle pdb=" S1  FES F 501 "
        pdb="FE2  FES F 501 "
        pdb=" S2  FES F 501 "
      ideal   model   delta    sigma   weight residual
     104.33   90.53   13.80 1.14e+00 7.69e-01 1.46e+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   89.13  -13.47 1.14e+00 7.69e-01 1.40e+02
  angle pdb=" S1  FES F 501 "
        pdb="FE1  FES F 501 "
        pdb=" S2  FES F 501 "
      ideal   model   delta    sigma   weight residual
     104.33   90.63   13.70 1.20e+00 6.94e-01 1.30e+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   88.67  -13.01 1.14e+00 7.69e-01 1.30e+02
  angle pdb=" S1  FES D 301 "
        pdb="FE2  FES D 301 "
        pdb=" S2  FES D 301 "
      ideal   model   delta    sigma   weight residual
     104.33   91.34   12.99 1.14e+00 7.69e-01 1.30e+02
  ... (remaining 20577 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.92: 8660
       29.92 -    59.85: 326
       59.85 -    89.77: 46
       89.77 -   119.70: 13
      119.70 -   149.62: 3
  Dihedral angle restraints: 9048
    sinusoidal: 3682
      harmonic: 5366
  Sorted by residual:
  dihedral pdb=" CA  HIS A 215 "
           pdb=" C   HIS A 215 "
           pdb=" N   PRO A 216 "
           pdb=" CA  PRO A 216 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  119.33   60.67     0      5.00e+00 4.00e-02 1.47e+02
  dihedral pdb=" C   ILE B 272 "
           pdb=" N   ILE B 272 "
           pdb=" CA  ILE B 272 "
           pdb=" CB  ILE B 272 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.12   14.12     0      2.50e+00 1.60e-01 3.19e+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 -152.83  -27.17     0      5.00e+00 4.00e-02 2.95e+01
  ... (remaining 9045 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 2131
       0.088 -    0.177: 165
       0.177 -    0.265: 16
       0.265 -    0.353: 6
       0.353 -    0.441: 5
  Chirality restraints: 2323
  Sorted by residual:
  chirality pdb=" CA  THR C 173 "
            pdb=" N   THR C 173 "
            pdb=" C   THR C 173 "
            pdb=" CB  THR C 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.08    0.44 2.00e-01 2.50e+01 4.87e+00
  chirality pdb=" CB  ILE B 220 "
            pdb=" CA  ILE B 220 "
            pdb=" CG1 ILE B 220 "
            pdb=" CG2 ILE B 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.24    0.41 2.00e-01 2.50e+01 4.11e+00
  chirality pdb=" CA  ILE B 272 "
            pdb=" N   ILE B 272 "
            pdb=" C   ILE B 272 "
            pdb=" CB  ILE B 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.06    0.38 2.00e-01 2.50e+01 3.57e+00
  ... (remaining 2320 not shown)

  Planarity restraints: 2573
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' FMN C 301 "    0.060 2.00e-02 2.50e+03   2.69e-02 3.27e+01
        pdb=" C10 FMN C 301 "    0.007 2.00e-02 2.50e+03
        pdb=" C2  FMN C 301 "   -0.025 2.00e-02 2.50e+03
        pdb=" C4  FMN C 301 "    0.019 2.00e-02 2.50e+03
        pdb=" C4A FMN C 301 "    0.020 2.00e-02 2.50e+03
        pdb=" C5A FMN C 301 "    0.020 2.00e-02 2.50e+03
        pdb=" C6  FMN C 301 "    0.021 2.00e-02 2.50e+03
        pdb=" C7  FMN C 301 "   -0.016 2.00e-02 2.50e+03
        pdb=" C7M FMN C 301 "   -0.035 2.00e-02 2.50e+03
        pdb=" C8  FMN C 301 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8M FMN C 301 "   -0.026 2.00e-02 2.50e+03
        pdb=" C9  FMN C 301 "    0.011 2.00e-02 2.50e+03
        pdb=" C9A FMN C 301 "    0.014 2.00e-02 2.50e+03
        pdb=" N1  FMN C 301 "   -0.014 2.00e-02 2.50e+03
        pdb=" N10 FMN C 301 "    0.000 2.00e-02 2.50e+03
        pdb=" N3  FMN C 301 "   -0.004 2.00e-02 2.50e+03
        pdb=" N5  FMN C 301 "    0.026 2.00e-02 2.50e+03
        pdb=" O2  FMN C 301 "   -0.057 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 215 "    0.064 5.00e-02 4.00e+02   9.58e-02 1.47e+01
        pdb=" N   PRO A 216 "   -0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO A 216 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A 216 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 167 "    0.019 2.00e-02 2.50e+03   3.47e-02 1.21e+01
        pdb=" C   ALA B 167 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   ALA B 167 "    0.021 2.00e-02 2.50e+03
        pdb=" N   LEU B 168 "    0.021 2.00e-02 2.50e+03
  ... (remaining 2570 not shown)

  Histogram of nonbonded interaction distances:
        1.03 -     1.80: 3
        1.80 -     2.58: 93
        2.58 -     3.35: 17851
        3.35 -     4.13: 34936
        4.13 -     4.90: 67591
  Nonbonded interactions: 120474
  Sorted by model distance:
  nonbonded pdb=" SD  MET E  17 "
            pdb="CA    CA E 201 "
     model   vdw
     1.026 2.870
  nonbonded pdb=" CE  MET E  17 "
            pdb="CA    CA E 201 "
     model   vdw
     1.259 2.930
  nonbonded pdb=" CG  MET E  17 "
            pdb="CA    CA E 201 "
     model   vdw
     1.491 2.910
  nonbonded pdb=" O   PHE E  28 "
            pdb=" OG  SER E  32 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" CB  MET E  17 "
            pdb="CA    CA E 201 "
     model   vdw
     2.237 2.910
  ... (remaining 120469 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     16.290
  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:             0.010
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
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      :  0.020   1.065  15195  Z= 0.609
  Angle     :  1.146  53.069  20594  Z= 0.576
  Chirality :  0.054   0.441   2323
  Planarity :  0.005   0.096   2573
  Dihedral  : 16.508 149.622   5626
  Min Nonbonded Distance : 1.026

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.29 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  4.21 %
    Favored  : 95.21 %
  Cbeta Deviations :  0.35 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.19 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.17), residues: 1885
  helix: -0.76 (0.16), residues: 857
  sheet: -2.45 (0.34), residues: 174
  loop : -2.48 (0.17), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 199 
 TYR   0.017   0.001   TYR B 216 
 PHE   0.020   0.001   PHE B 342 
 TRP   0.021   0.002   TRP B 103 
 HIS   0.006   0.001   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00752 (15185)
  covalent geometry    : angle       0.95846 (20582)
  hydrogen bonds       : bond        0.16269 (  686)
  hydrogen bonds       : angle       6.47225 ( 2001)
  metal coordination   : bond        0.78409 (    8)
  metal coordination   : angle      26.06975 (   12)
  Misc. bond           : bond        0.04189 (    2)

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

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

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 213
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8111 (ttpp)
REVERT: A  249 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8258 (mm-40)
REVERT: A  279 MET cc_start: 0.9085 (ttt) cc_final: 0.8848 (ttp)
REVERT: A  342 LYS cc_start: 0.8235 (tttm) cc_final: 0.7798 (ttpp)
REVERT: A  401 ASP cc_start: 0.7972 (t0) cc_final: 0.7677 (t70)
REVERT: B  380 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.7670 (tm-30)
REVERT: C   46 GLN cc_start: 0.8368 (mt0) cc_final: 0.8150 (mt0)
REVERT: C  129 ASP cc_start: 0.7613 (p0) cc_final: 0.7195 (p0)
REVERT: D  123 MET cc_start: 0.8523 (mmm) cc_final: 0.8310 (mmm)
REVERT: D  146 MET cc_start: 0.8370 (mmm) cc_final: 0.8050 (mmm)
REVERT: D  209 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.5742 (tmtt)
REVERT: E   33 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8351 (mttt)
REVERT: E  162 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7643 (mt-10)
REVERT: F   34 ASP cc_start: 0.7227 (p0) cc_final: 0.6729 (p0)
REVERT: F  252 LEU cc_start: 0.8092 (mm) cc_final: 0.7851 (mm)
  outliers start: 9
  outliers final: 2
  residues processed: 220
  average time/residue: 0.1285
  time to fit residues: 40.8604
Evaluate side-chains
  176 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 172
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  380 GLU
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain D residue  209 LYS
Chi-restraints excluded: chain D residue  210 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.2980
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    7.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A  44 HIS
A  88 GLN
A 109 GLN
** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 225 HIS
A 249 GLN
B  74 ASN
B  78 GLN
B  91 GLN
B 178 GLN
B 219 GLN
B 240 GLN
B 243 GLN
B 313 ASN
B 354 ASN
C  37 GLN
C  68 ASN
C  79 ASN
C 143 ASN
D 176 GLN
E  79 ASN
** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 295 GLN
** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 336 HIS

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.167952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.130955 restraints weight = 31167.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.52
r_work: 0.3207 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3058
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3058
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8828
moved from start:          0.0904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  15195  Z= 0.201
  Angle     :  0.639  14.194  20594  Z= 0.310
  Chirality :  0.045   0.179   2323
  Planarity :  0.005   0.094   2573
  Dihedral  : 13.376 168.940   2318
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.45 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  9.19 %
    Favored  : 89.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.19 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.18), residues: 1885
  helix:  0.31 (0.18), residues: 867
  sheet: -1.64 (0.39), residues: 172
  loop : -1.97 (0.19), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 199 
 TYR   0.014   0.002   TYR D 141 
 PHE   0.017   0.001   PHE E  28 
 TRP   0.022   0.002   TRP B 103 
 HIS   0.008   0.001   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (15185)
  covalent geometry    : angle       0.60398 (20582)
  hydrogen bonds       : bond        0.05549 (  686)
  hydrogen bonds       : angle       4.93295 ( 2001)
  metal coordination   : bond        0.02246 (    8)
  metal coordination   : angle       8.71260 (   12)
  Misc. bond           : bond        0.00097 (    2)

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

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

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 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: 15
    poor density    : 178
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8488 (ttpp)
REVERT: A   97 ASP cc_start: 0.7964 (p0) cc_final: 0.7442 (p0)
REVERT: A  342 LYS cc_start: 0.8830 (tttm) cc_final: 0.8315 (ttpp)
REVERT: B  380 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.7238 (tm-30)
REVERT: B  382 MET cc_start: 0.8747 (tpt) cc_final: 0.7881 (tpt)
REVERT: D  146 MET cc_start: 0.8637 (mmm) cc_final: 0.8314 (mmm)
REVERT: D  210 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.5037 (mm-30)
REVERT: E   33 LYS cc_start: 0.8838 (mtpp) cc_final: 0.8531 (mttt)
REVERT: E  162 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8461 (mt-10)
  outliers start: 15
  outliers final: 11
  residues processed: 188
  average time/residue: 0.1179
  time to fit residues: 33.1432
Evaluate side-chains
  186 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 173
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 GLN
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  380 GLU
Chi-restraints excluded: chain C residue   79 ASN
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain D residue   99 LYS
Chi-restraints excluded: chain D residue  210 GLU
Chi-restraints excluded: chain F residue  347 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 180 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   chunk 121 optimal weight:    1.9990
   chunk 149 optimal weight:    6.9990
   chunk 82 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 109 GLN
** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 199 HIS
** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  97 HIS
F 140 ASN
** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 332 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 = 0.3763 r_free = 0.3763 target = 0.158071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.119378 restraints weight = 30643.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 2.14
r_work: 0.3073 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3092
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3092
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.1073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15195  Z= 0.179
  Angle     :  0.602  15.501  20594  Z= 0.293
  Chirality :  0.044   0.167   2323
  Planarity :  0.005   0.090   2573
  Dihedral  : 12.340 169.235   2313
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.19 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 10.10 %
    Favored  : 88.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.19 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.19), residues: 1885
  helix:  0.73 (0.18), residues: 868
  sheet: -1.06 (0.42), residues: 145
  loop : -1.82 (0.19), residues: 872

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 199 
 TYR   0.013   0.001   TYR D 141 
 PHE   0.015   0.001   PHE E  28 
 TRP   0.022   0.001   TRP B 103 
 HIS   0.008   0.001   HIS F 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (15185)
  covalent geometry    : angle       0.57396 (20582)
  hydrogen bonds       : bond        0.05205 (  686)
  hydrogen bonds       : angle       4.75046 ( 2001)
  metal coordination   : bond        0.01125 (    8)
  metal coordination   : angle       7.51638 (   12)
  Misc. bond           : bond        0.00092 (    2)

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

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

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 180
  time to evaluate  : 0.607 
Fit side-chains
REVERT: A   75 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8312 (ttpp)
REVERT: A   97 ASP cc_start: 0.7686 (p0) cc_final: 0.7202 (p0)
REVERT: A  342 LYS cc_start: 0.8657 (tttm) cc_final: 0.8132 (ttpp)
REVERT: B  380 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.7201 (tm-30)
REVERT: D  210 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.5407 (mm-30)
REVERT: E   33 LYS cc_start: 0.8752 (mtpp) cc_final: 0.8444 (mttt)
REVERT: E  162 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8305 (mt-10)
REVERT: E  197 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8474 (mm-40)
  outliers start: 23
  outliers final: 16
  residues processed: 192
  average time/residue: 0.1136
  time to fit residues: 32.9211
Evaluate side-chains
  192 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 173
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 GLN
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  380 GLU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain D residue   71 ARG
Chi-restraints excluded: chain D residue   99 LYS
Chi-restraints excluded: chain D residue  210 GLU
Chi-restraints excluded: chain E residue  197 GLN
Chi-restraints excluded: chain F residue   27 SER
Chi-restraints excluded: chain F residue  175 HIS
Chi-restraints excluded: chain F residue  347 ASN
Chi-restraints excluded: chain F residue  349 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 141 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 131 optimal weight:    0.6980
   chunk 174 optimal weight:    7.9990
   chunk 129 optimal weight:    0.6980
   chunk 144 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0070
   chunk 157 optimal weight:    9.9990
   chunk 46 optimal weight:    0.5980
   chunk 155 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.0000

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

Flipped N/Q/H residues before XYZ refinement:
** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 199 HIS
** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.159715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.121880 restraints weight = 24038.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.79
r_work: 0.3159 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8742
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15195  Z= 0.127
  Angle     :  0.549  12.971  20594  Z= 0.269
  Chirality :  0.042   0.205   2323
  Planarity :  0.005   0.120   2573
  Dihedral  : 10.720 158.545   2313
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.98 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.33 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.19 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.19), residues: 1885
  helix:  1.04 (0.18), residues: 875
  sheet: -0.84 (0.43), residues: 145
  loop : -1.64 (0.19), residues: 865

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  43 
 TYR   0.014   0.001   TYR D 141 
 PHE   0.014   0.001   PHE E  28 
 TRP   0.021   0.001   TRP B 103 
 HIS   0.008   0.001   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (15185)
  covalent geometry    : angle       0.52756 (20582)
  hydrogen bonds       : bond        0.04537 (  686)
  hydrogen bonds       : angle       4.56647 ( 2001)
  metal coordination   : bond        0.00752 (    8)
  metal coordination   : angle       6.31074 (   12)
  Misc. bond           : bond        0.00053 (    2)

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

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

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 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: 25
    poor density    : 175
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8344 (ttpp)
REVERT: A   97 ASP cc_start: 0.7755 (p0) cc_final: 0.7265 (p0)
REVERT: A  342 LYS cc_start: 0.8675 (tttm) cc_final: 0.8128 (ttpp)
REVERT: D  210 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.5367 (mm-30)
REVERT: E   33 LYS cc_start: 0.8806 (mtpp) cc_final: 0.8547 (mttt)
REVERT: E  162 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8367 (mt-10)
REVERT: E  197 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8489 (mm-40)
  outliers start: 25
  outliers final: 15
  residues processed: 189
  average time/residue: 0.1143
  time to fit residues: 32.7433
Evaluate side-chains
  187 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 170
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain D residue   71 ARG
Chi-restraints excluded: chain D residue   99 LYS
Chi-restraints excluded: chain D residue  210 GLU
Chi-restraints excluded: chain E residue  197 GLN
Chi-restraints excluded: chain F residue   27 SER
Chi-restraints excluded: chain F residue  175 HIS
Chi-restraints excluded: chain F residue  349 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 141 optimal weight:    6.9990
   chunk 137 optimal weight:    7.9990
   chunk 86 optimal weight:    0.9980
   chunk 144 optimal weight:    1.9990
   chunk 184 optimal weight:    5.9990
   chunk 143 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 154 optimal weight:    7.9990
   chunk 116 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 128 optimal weight:    0.7980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
C 199 HIS
** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 176 HIS
F 347 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.160170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.123356 restraints weight = 31067.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.31
r_work: 0.3117 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2985
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2985
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8793
moved from start:          0.1347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15195  Z= 0.142
  Angle     :  0.540  12.292  20594  Z= 0.266
  Chirality :  0.042   0.197   2323
  Planarity :  0.005   0.108   2573
  Dihedral  :  9.730 103.660   2310
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.35 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 12.30 %
    Favored  : 86.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.19 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.19), residues: 1885
  helix:  1.19 (0.18), residues: 873
  sheet: -0.67 (0.44), residues: 143
  loop : -1.52 (0.19), residues: 869

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  43 
 TYR   0.013   0.001   TYR F 217 
 PHE   0.014   0.001   PHE E  28 
 TRP   0.021   0.001   TRP B 103 
 HIS   0.007   0.001   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (15185)
  covalent geometry    : angle       0.52122 (20582)
  hydrogen bonds       : bond        0.04632 (  686)
  hydrogen bonds       : angle       4.51773 ( 2001)
  metal coordination   : bond        0.00630 (    8)
  metal coordination   : angle       5.93187 (   12)
  Misc. bond           : bond        0.00070 (    2)

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

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

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 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: 24
    poor density    : 173
  time to evaluate  : 0.579 
Fit side-chains
REVERT: A   75 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8396 (ttpp)
REVERT: A   97 ASP cc_start: 0.7845 (p0) cc_final: 0.7357 (p0)
REVERT: A  342 LYS cc_start: 0.8765 (tttm) cc_final: 0.8232 (ttpp)
REVERT: E   33 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8585 (mttt)
REVERT: E  162 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8461 (mt-10)
REVERT: E  197 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8541 (mm-40)
  outliers start: 24
  outliers final: 19
  residues processed: 186
  average time/residue: 0.1104
  time to fit residues: 31.0798
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  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain D residue   99 LYS
Chi-restraints excluded: chain D residue  169 ILE
Chi-restraints excluded: chain E residue  197 GLN
Chi-restraints excluded: chain F residue   27 SER
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain F residue  175 HIS
Chi-restraints excluded: chain F residue  349 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 181 optimal weight:    9.9990
   chunk 62 optimal weight:    3.9990
   chunk 135 optimal weight:    0.9990
   chunk 27 optimal weight:    0.2980
   chunk 19 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   chunk 155 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0670
   chunk 54 optimal weight:    3.9990
   chunk 127 optimal weight:    4.9990
   overall best weight:    1.4724

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

Flipped N/Q/H residues before XYZ refinement:
B 404 ASN
C 199 HIS
** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.159202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.120131 restraints weight = 28152.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 2.03
r_work: 0.3094 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2983
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2983
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8791
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  15195  Z= 0.154
  Angle     :  0.548  11.439  20594  Z= 0.272
  Chirality :  0.043   0.207   2323
  Planarity :  0.005   0.103   2573
  Dihedral  :  9.190  83.637   2307
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.35 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 12.75 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.19 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.19), residues: 1885
  helix:  1.22 (0.18), residues: 875
  sheet: -0.57 (0.45), residues: 143
  loop : -1.42 (0.20), residues: 867

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  43 
 TYR   0.013   0.001   TYR E 134 
 PHE   0.016   0.001   PHE E  28 
 TRP   0.022   0.001   TRP B 103 
 HIS   0.007   0.001   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (15185)
  covalent geometry    : angle       0.53067 (20582)
  hydrogen bonds       : bond        0.04737 (  686)
  hydrogen bonds       : angle       4.49837 ( 2001)
  metal coordination   : bond        0.00601 (    8)
  metal coordination   : angle       5.68337 (   12)
  Misc. bond           : bond        0.00076 (    2)

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

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

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 174
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8343 (ttpp)
REVERT: A   97 ASP cc_start: 0.7850 (p0) cc_final: 0.7367 (p0)
REVERT: A  342 LYS cc_start: 0.8766 (tttm) cc_final: 0.8217 (ttpp)
REVERT: B  380 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.7109 (tm-30)
REVERT: E   33 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8586 (mttt)
REVERT: E  162 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8487 (mt-10)
REVERT: E  197 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8518 (mm-40)
REVERT: F  377 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8647 (ttp)
  outliers start: 24
  outliers final: 20
  residues processed: 186
  average time/residue: 0.1173
  time to fit residues: 32.8358
Evaluate side-chains
  196 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 173
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  380 GLU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain D residue   99 LYS
Chi-restraints excluded: chain D residue  132 ILE
Chi-restraints excluded: chain D residue  169 ILE
Chi-restraints excluded: chain E residue  197 GLN
Chi-restraints excluded: chain F residue   27 SER
Chi-restraints excluded: chain F residue   97 HIS
Chi-restraints excluded: chain F residue  175 HIS
Chi-restraints excluded: chain F residue  349 THR
Chi-restraints excluded: chain F residue  377 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 137 optimal weight:    2.9990
   chunk 176 optimal weight:    8.9990
   chunk 67 optimal weight:    3.9990
   chunk 103 optimal weight:    7.9990
   chunk 1 optimal weight:    0.0040
   chunk 49 optimal weight:    0.9990
   chunk 95 optimal weight:    7.9990
   chunk 101 optimal weight:    2.9990
   chunk 147 optimal weight:   10.0000
   overall best weight:    2.0000

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

Flipped N/Q/H residues before XYZ refinement:
A 109 GLN
C 199 HIS
C 216 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.158005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.119143 restraints weight = 35301.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.60
r_work: 0.3037 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.1441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  15195  Z= 0.194
  Angle     :  0.578  11.634  20594  Z= 0.286
  Chirality :  0.044   0.176   2323
  Planarity :  0.005   0.135   2573
  Dihedral  :  9.205  87.756   2307
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.45 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.69 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.19 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.19), residues: 1885
  helix:  1.20 (0.18), residues: 872
  sheet: -0.57 (0.45), residues: 143
  loop : -1.38 (0.20), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  43 
 TYR   0.012   0.002   TYR F 217 
 PHE   0.017   0.001   PHE E  28 
 TRP   0.022   0.002   TRP B 103 
 HIS   0.006   0.001   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 (15185)
  covalent geometry    : angle       0.56080 (20582)
  hydrogen bonds       : bond        0.05136 (  686)
  hydrogen bonds       : angle       4.56612 ( 2001)
  metal coordination   : bond        0.00668 (    8)
  metal coordination   : angle       5.83873 (   12)
  Misc. bond           : bond        0.00108 (    2)

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

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

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 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: 30
    poor density    : 174
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A   75 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8315 (ttpp)
REVERT: A   97 ASP cc_start: 0.7713 (p0) cc_final: 0.7233 (p0)
REVERT: A  342 LYS cc_start: 0.8690 (tttm) cc_final: 0.8151 (ttpp)
REVERT: B  380 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.7189 (tm-30)
REVERT: E   17 MET cc_start: 0.8365 (mmm) cc_final: 0.7875 (mmm)
REVERT: E   33 LYS cc_start: 0.8806 (mtpp) cc_final: 0.8569 (mttt)
REVERT: E  162 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8314 (mt-10)
REVERT: E  197 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8509 (mm-40)
REVERT: F  377 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8490 (ttp)
  outliers start: 30
  outliers final: 22
  residues processed: 190
  average time/residue: 0.1128
  time to fit residues: 32.2537
Evaluate side-chains
  197 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 172
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 GLN
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  380 GLU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain D residue   99 LYS
Chi-restraints excluded: chain D residue  132 ILE
Chi-restraints excluded: chain D residue  169 ILE
Chi-restraints excluded: chain E residue  197 GLN
Chi-restraints excluded: chain F residue   27 SER
Chi-restraints excluded: chain F residue   97 HIS
Chi-restraints excluded: chain F residue  175 HIS
Chi-restraints excluded: chain F residue  349 THR
Chi-restraints excluded: chain F residue  377 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 147 optimal weight:   10.0000
   chunk 0 optimal weight:    4.9990
   chunk 166 optimal weight:    0.8980
   chunk 122 optimal weight:    6.9990
   chunk 157 optimal weight:   20.0000
   chunk 145 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 146 optimal weight:    7.9990
   chunk 178 optimal weight:    1.9990
   chunk 171 optimal weight:   10.0000
   chunk 148 optimal weight:    7.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 109 GLN
A 368 ASN
C 199 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.166893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.129841 restraints weight = 30258.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 2.53
r_work: 0.3186 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  15195  Z= 0.223
  Angle     :  0.598  11.848  20594  Z= 0.297
  Chirality :  0.045   0.185   2323
  Planarity :  0.005   0.133   2573
  Dihedral  :  9.294  91.082   2307
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.77 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.46 %
    Favored  : 84.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.19 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.19), residues: 1885
  helix:  1.13 (0.18), residues: 872
  sheet: -0.59 (0.44), residues: 143
  loop : -1.34 (0.20), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  43 
 TYR   0.013   0.002   TYR F 179 
 PHE   0.018   0.002   PHE E  28 
 TRP   0.022   0.002   TRP B 103 
 HIS   0.006   0.001   HIS F 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 (15185)
  covalent geometry    : angle       0.58116 (20582)
  hydrogen bonds       : bond        0.05370 (  686)
  hydrogen bonds       : angle       4.61200 ( 2001)
  metal coordination   : bond        0.00720 (    8)
  metal coordination   : angle       5.86462 (   12)
  Misc. bond           : bond        0.00140 (    2)

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

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

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 173
  time to evaluate  : 0.520 
Fit side-chains
REVERT: A   75 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8313 (ttpp)
REVERT: A   97 ASP cc_start: 0.7732 (p0) cc_final: 0.7252 (p0)
REVERT: A  342 LYS cc_start: 0.8683 (tttm) cc_final: 0.8178 (ttpp)
REVERT: B  380 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.7350 (tm-30)
REVERT: E   17 MET cc_start: 0.8322 (mmm) cc_final: 0.7836 (mmm)
REVERT: E  197 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8485 (mm-40)
REVERT: F  377 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8376 (ttp)
  outliers start: 25
  outliers final: 22
  residues processed: 184
  average time/residue: 0.1172
  time to fit residues: 32.4726
Evaluate side-chains
  195 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 170
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 GLN
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  380 GLU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  129 ASP
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain D residue   99 LYS
Chi-restraints excluded: chain D residue  169 ILE
Chi-restraints excluded: chain E residue  197 GLN
Chi-restraints excluded: chain F residue   27 SER
Chi-restraints excluded: chain F residue   97 HIS
Chi-restraints excluded: chain F residue  175 HIS
Chi-restraints excluded: chain F residue  349 THR
Chi-restraints excluded: chain F residue  377 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 171 optimal weight:    9.9990
   chunk 66 optimal weight:    0.8980
   chunk 150 optimal weight:   10.0000
   chunk 85 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9980
   chunk 128 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 106 optimal weight:    6.9990
   chunk 60 optimal weight:    0.4980
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 109 GLN
A 215 HIS
C  79 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.160858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.123149 restraints weight = 25614.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 1.92
r_work: 0.3136 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8753
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15195  Z= 0.116
  Angle     :  0.520  11.163  20594  Z= 0.260
  Chirality :  0.042   0.158   2323
  Planarity :  0.005   0.120   2573
  Dihedral  :  8.845  80.838   2307
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.13 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 13.79 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.19 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.19), residues: 1885
  helix:  1.41 (0.18), residues: 870
  sheet: -0.48 (0.45), residues: 143
  loop : -1.21 (0.20), residues: 872

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  43 
 TYR   0.014   0.001   TYR D 141 
 PHE   0.014   0.001   PHE E  28 
 TRP   0.021   0.001   TRP B 103 
 HIS   0.009   0.001   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (15185)
  covalent geometry    : angle       0.50341 (20582)
  hydrogen bonds       : bond        0.04343 (  686)
  hydrogen bonds       : angle       4.43223 ( 2001)
  metal coordination   : bond        0.00567 (    8)
  metal coordination   : angle       5.41111 (   12)
  Misc. bond           : bond        0.00034 (    2)

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

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

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 179
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8310 (ttpp)
REVERT: A   97 ASP cc_start: 0.7795 (p0) cc_final: 0.7321 (p0)
REVERT: A  342 LYS cc_start: 0.8725 (tttm) cc_final: 0.8175 (ttpp)
REVERT: E   17 MET cc_start: 0.8439 (mmm) cc_final: 0.8121 (mmm)
REVERT: E  162 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8376 (mt-10)
REVERT: E  197 GLN cc_start: 0.8746 (mt0) cc_final: 0.8511 (mm-40)
REVERT: F   34 ASP cc_start: 0.7393 (p0) cc_final: 0.7042 (p0)
REVERT: F  112 GLN cc_start: 0.8060 (mp10) cc_final: 0.7086 (mp10)
REVERT: F  175 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.7367 (t-90)
REVERT: F  377 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8610 (ttp)
  outliers start: 22
  outliers final: 15
  residues processed: 187
  average time/residue: 0.1161
  time to fit residues: 32.8797
Evaluate side-chains
  191 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 174
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 GLN
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  129 ASP
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain D residue   99 LYS
Chi-restraints excluded: chain F residue  175 HIS
Chi-restraints excluded: chain F residue  349 THR
Chi-restraints excluded: chain F residue  377 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 160 optimal weight:    6.9990
   chunk 107 optimal weight:    0.7980
   chunk 128 optimal weight:    0.7980
   chunk 179 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.161014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.122178 restraints weight = 28207.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 2.05
r_work: 0.3117 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3023
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3023 r_free = 0.3023    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3023 r_free = 0.3023    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3023
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8769
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15195  Z= 0.114
  Angle     :  0.518  11.175  20594  Z= 0.258
  Chirality :  0.041   0.159   2323
  Planarity :  0.005   0.117   2573
  Dihedral  :  8.647  77.002   2307
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.98 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 14.30 %
    Favored  : 84.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.19 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.19), residues: 1885
  helix:  1.51 (0.18), residues: 870
  sheet: -0.48 (0.45), residues: 143
  loop : -1.12 (0.20), residues: 872

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  43 
 TYR   0.014   0.001   TYR D 141 
 PHE   0.014   0.001   PHE E  28 
 TRP   0.022   0.001   TRP B 103 
 HIS   0.007   0.001   HIS F 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (15185)
  covalent geometry    : angle       0.50269 (20582)
  hydrogen bonds       : bond        0.04251 (  686)
  hydrogen bonds       : angle       4.37755 ( 2001)
  metal coordination   : bond        0.00534 (    8)
  metal coordination   : angle       5.22177 (   12)
  Misc. bond           : bond        0.00035 (    2)

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

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

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3770 Ramachandran restraints generated.
    1885 Oldfield, 0 Emsley, 1885 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: 18
    poor density    : 179
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8324 (ttpp)
REVERT: A   97 ASP cc_start: 0.7826 (p0) cc_final: 0.7350 (p0)
REVERT: A  342 LYS cc_start: 0.8769 (tttm) cc_final: 0.8221 (ttpp)
REVERT: D  194 MET cc_start: 0.9042 (mtp) cc_final: 0.8833 (ttt)
REVERT: D  209 LYS cc_start: 0.7234 (tmtt) cc_final: 0.6916 (tptm)
REVERT: E   17 MET cc_start: 0.8481 (mmm) cc_final: 0.8188 (mmm)
REVERT: E  162 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8432 (mt-10)
REVERT: E  197 GLN cc_start: 0.8688 (mt0) cc_final: 0.8465 (mm-40)
REVERT: F  112 GLN cc_start: 0.8065 (mp10) cc_final: 0.7099 (mp10)
REVERT: F  175 HIS cc_start: 0.7727 (OUTLIER) cc_final: 0.7402 (t-90)
REVERT: F  377 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8662 (ttp)
  outliers start: 18
  outliers final: 16
  residues processed: 185
  average time/residue: 0.1144
  time to fit residues: 31.9814
Evaluate side-chains
  194 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 176
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  129 ASP
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain D residue   99 LYS
Chi-restraints excluded: chain F residue  175 HIS
Chi-restraints excluded: chain F residue  347 ASN
Chi-restraints excluded: chain F residue  349 THR
Chi-restraints excluded: chain F residue  377 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 159 optimal weight:   10.0000
   chunk 102 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 168 optimal weight:    0.9980
   chunk 114 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 148 optimal weight:    1.9990
   chunk 143 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    1.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.160295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.123862 restraints weight = 25776.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.82
r_work: 0.3150 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8769
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15195  Z= 0.144
  Angle     :  0.534  11.106  20594  Z= 0.267
  Chirality :  0.042   0.153   2323
  Planarity :  0.005   0.117   2573
  Dihedral  :  8.667  78.022   2307
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.08 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.30 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.19 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.19), residues: 1885
  helix:  1.46 (0.18), residues: 870
  sheet: -0.41 (0.45), residues: 141
  loop : -1.09 (0.20), residues: 874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  43 
 TYR   0.013   0.001   TYR F 217 
 PHE   0.015   0.001   PHE E  28 
 TRP   0.022   0.001   TRP B 103 
 HIS   0.007   0.001   HIS F 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (15185)
  covalent geometry    : angle       0.51918 (20582)
  hydrogen bonds       : bond        0.04553 (  686)
  hydrogen bonds       : angle       4.40190 ( 2001)
  metal coordination   : bond        0.00591 (    8)
  metal coordination   : angle       5.19451 (   12)
  Misc. bond           : bond        0.00073 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3667.46 seconds
wall clock time: 63 minutes 20.06 seconds (3800.06 seconds total)