Starting phenix.real_space_refine
on Tue Jun 17 21:32:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8thd_41254/06_2025/8thd_41254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8thd_41254/06_2025/8thd_41254.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8thd_41254/06_2025/8thd_41254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8thd_41254/06_2025/8thd_41254.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8thd_41254/06_2025/8thd_41254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8thd_41254/06_2025/8thd_41254.cif"
  }
  resolution = 3.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      14      5.49       5
     Mg      3      5.21       5
     S      98      5.16       5
     C   12905      2.51       5
     N    3437      2.21       5
     O    3939      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 20396
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 3863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 474, 3863
          Classifications: {'peptide': 474}
          Link IDs: {'PTRANS': 21, 'TRANS': 452}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 2495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2495
          Classifications: {'peptide': 318}
          Link IDs: {'PTRANS': 9, 'TRANS': 308}
    Chain: "C"
      Number of atoms: 2571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2571
          Classifications: {'peptide': 325}
          Link IDs: {'PTRANS': 12, 'TRANS': 312}
    Chain: "D"
      Number of atoms: 2629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2629
          Classifications: {'peptide': 332}
          Link IDs: {'PTRANS': 12, 'TRANS': 319}
    Chain: "E"
      Number of atoms: 2675
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2675
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 14, 'TRANS': 324}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1995
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1995
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 8, 'TRANS': 245}
    Chain: "G"
      Number of atoms: 2011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 2011
          Classifications: {'peptide': 256}
          Link IDs: {'PTRANS': 8, 'TRANS': 247}
    Chain: "H"
      Number of atoms: 2003
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 2003
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 8, 'TRANS': 246}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'AGS': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 13.13, per 1000 atoms: 0.64
  Number of scatterers: 20396
  At special positions: 0
  Unit cell: (115.92, 119.232, 150.696, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      98     16.00
     P      14     15.00
     Mg      3     11.99
     O    3939      8.00
     N    3437      7.00
     C   12905      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 5.68
  Conformation dependent library (CDL) restraints added in 3.0 seconds
  

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4898

  Finding SS restraints...
    Secondary structure from input PDB file:
      106 helices and 16 sheets defined
      50.0% alpha, 14.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 203 through 209
    Processing helix  chain 'A' and resid 240 through 245
    Processing helix  chain 'A' and resid 256 through 276
      removed outlier: 3.586A  pdb=" N   LYS A 276 " --> pdb=" O   HIS A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 356
    Processing helix  chain 'A' and resid 373 through 387
      removed outlier: 6.616A  pdb=" N   ASP A 379 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   ILE A 380 " --> pdb=" O   ASP A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 429
    Processing helix  chain 'A' and resid 445 through 455
      removed outlier: 3.514A  pdb=" N   GLN A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 481
      removed outlier: 3.521A  pdb=" N   VAL A 469 " --> pdb=" O   SER A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 496
    Processing helix  chain 'A' and resid 499 through 511
    Processing helix  chain 'A' and resid 535 through 557
      removed outlier: 3.660A  pdb=" N   ILE A 539 " --> pdb=" O   SER A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 581
    Processing helix  chain 'A' and resid 585 through 592
      removed outlier: 3.518A  pdb=" N   PHE A 592 " --> pdb=" O   MET A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 629
      removed outlier: 3.786A  pdb=" N   HIS A 620 " --> pdb=" O   ASN A 616 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ARG A 628 " --> pdb=" O   GLN A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 639
      removed outlier: 3.996A  pdb=" N   ARG A 633 " --> pdb=" O   TYR A 629 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   HIS A 637 " --> pdb=" O   ARG A 633 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   LEU A 639 " --> pdb=" O   ALA A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 645 through 661
    Processing helix  chain 'A' and resid 700 through 708
      removed outlier: 4.138A  pdb=" N   LEU A 706 " --> pdb=" O   GLU A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 716
    Processing helix  chain 'A' and resid 716 through 735
    Processing helix  chain 'A' and resid 773 through 781
    Processing helix  chain 'B' and resid 10 through 15
    Processing helix  chain 'B' and resid 26 through 40
    Processing helix  chain 'B' and resid 54 through 68
    Processing helix  chain 'B' and resid 70 through 74
    Processing helix  chain 'B' and resid 85 through 99
      removed outlier: 4.052A  pdb=" N   ILE B  93 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   LYS B  94 " --> pdb=" O   ARG B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 119
    Processing helix  chain 'B' and resid 120 through 134
      removed outlier: 4.027A  pdb=" N   ARG B 129 " --> pdb=" O   GLN B 125 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   THR B 130 " --> pdb=" O   ALA B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 150
      removed outlier: 3.742A  pdb=" N   LYS B 149 " --> pdb=" O   GLN B 146 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ILE B 150 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 146 through 150'
    Processing helix  chain 'B' and resid 151 through 156
    Processing helix  chain 'B' and resid 167 through 183
    Processing helix  chain 'B' and resid 187 through 199
    Processing helix  chain 'B' and resid 201 through 217
    Processing helix  chain 'B' and resid 220 through 225
    Processing helix  chain 'B' and resid 232 through 242
    Processing helix  chain 'B' and resid 244 through 255
    Processing helix  chain 'B' and resid 262 through 277
    Processing helix  chain 'B' and resid 281 through 302
    Processing helix  chain 'B' and resid 305 through 322
      removed outlier: 3.786A  pdb=" N   LEU B 309 " --> pdb=" O   THR B 305 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 19
    Processing helix  chain 'C' and resid 23 through 27
      removed outlier: 3.671A  pdb=" N   VAL C  27 " --> pdb=" O   LEU C  24 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 44
    Processing helix  chain 'C' and resid 58 through 72
    Processing helix  chain 'C' and resid 74 through 78
    Processing helix  chain 'C' and resid 88 through 102
      removed outlier: 3.871A  pdb=" N   VAL C  92 " --> pdb=" O   ARG C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 137
    Processing helix  chain 'C' and resid 149 through 153
      removed outlier: 3.735A  pdb=" N   LYS C 152 " --> pdb=" O   TYR C 149 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU C 153 " --> pdb=" O   ALA C 150 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 149 through 153'
    Processing helix  chain 'C' and resid 154 through 159
    Processing helix  chain 'C' and resid 170 through 186
      removed outlier: 3.525A  pdb=" N   HIS C 184 " --> pdb=" O   ASN C 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 202
      removed outlier: 3.923A  pdb=" N   ASN C 202 " --> pdb=" O   ILE C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 219
    Processing helix  chain 'C' and resid 228 through 236
      removed outlier: 3.574A  pdb=" N   ILE C 232 " --> pdb=" O   SER C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 240 through 254
    Processing helix  chain 'C' and resid 255 through 271
    Processing helix  chain 'C' and resid 273 through 288
      removed outlier: 3.651A  pdb=" N   ASP C 287 " --> pdb=" O   LYS C 283 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   TYR C 288 " --> pdb=" O   ILE C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 293 through 313
    Processing helix  chain 'C' and resid 315 through 334
      removed outlier: 3.578A  pdb=" N   GLU C 334 " --> pdb=" O   SER C 330 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 31
    Processing helix  chain 'D' and resid 42 through 55
      removed outlier: 4.124A  pdb=" N   VAL D  48 " --> pdb=" O   HIS D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 71 through 83
    Processing helix  chain 'D' and resid 84 through 92
      removed outlier: 4.344A  pdb=" N   LYS D  89 " --> pdb=" O   PRO D  85 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   SER D  90 " --> pdb=" O   ASP D  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 115
    Processing helix  chain 'D' and resid 153 through 160
    Processing helix  chain 'D' and resid 193 through 208
    Processing helix  chain 'D' and resid 215 through 225
    Processing helix  chain 'D' and resid 227 through 246
    Processing helix  chain 'D' and resid 252 through 261
      removed outlier: 3.519A  pdb=" N   VAL D 256 " --> pdb=" O   THR D 252 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 264 through 278
    Processing helix  chain 'D' and resid 279 through 292
      removed outlier: 3.844A  pdb=" N   LYS D 292 " --> pdb=" O   ASN D 288 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 296 through 310
      removed outlier: 3.563A  pdb=" N   VAL D 300 " --> pdb=" O   SER D 296 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   THR D 310 " --> pdb=" O   GLU D 306 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 315 through 335
      removed outlier: 3.589A  pdb=" N   TRP D 324 " --> pdb=" O   ASN D 320 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 338 through 353
    Processing helix  chain 'E' and resid 3 through 8
    Processing helix  chain 'E' and resid 19 through 32
      removed outlier: 3.897A  pdb=" N   GLN E  32 " --> pdb=" O   SER E  28 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 48 through 61
    Processing helix  chain 'E' and resid 62 through 67
    Processing helix  chain 'E' and resid 97 through 105
      removed outlier: 7.971A  pdb=" N   ASN E 103 " --> pdb=" O   ASP E 100 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ASN E 104 " --> pdb=" O   MET E 101 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 106 through 119
      removed outlier: 4.044A  pdb=" N   MET E 119 " --> pdb=" O   GLU E 115 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 143 through 146
    Processing helix  chain 'E' and resid 147 through 161
      removed outlier: 3.517A  pdb=" N   GLU E 159 " --> pdb=" O   ARG E 155 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 178 through 184
    Processing helix  chain 'E' and resid 194 through 210
    Processing helix  chain 'E' and resid 216 through 227
      removed outlier: 3.720A  pdb=" N   LYS E 220 " --> pdb=" O   LYS E 216 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 229 through 245
    Processing helix  chain 'E' and resid 257 through 273
    Processing helix  chain 'E' and resid 275 through 292
    Processing helix  chain 'E' and resid 295 through 308
    Processing helix  chain 'E' and resid 314 through 334
    Processing helix  chain 'E' and resid 337 through 354
      removed outlier: 4.092A  pdb=" N   HIS E 341 " --> pdb=" O   LYS E 337 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ASP E 354 " --> pdb=" O   MET E 350 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 8 through 19
      removed outlier: 4.257A  pdb=" N   PHE F  12 " --> pdb=" O   GLU F   8 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE F  19 " --> pdb=" O   ILE F  15 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 72 through 81
    Processing helix  chain 'F' and resid 141 through 155
      removed outlier: 3.624A  pdb=" N   GLN F 153 " --> pdb=" O   ARG F 149 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   LEU F 154 " --> pdb=" O   ASP F 150 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER F 155 " --> pdb=" O   LEU F 151 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 163 through 166
    Processing helix  chain 'F' and resid 209 through 216
    Processing helix  chain 'F' and resid 217 through 221
      removed outlier: 3.812A  pdb=" N   SER F 220 " --> pdb=" O   LYS F 217 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 21
      removed outlier: 3.507A  pdb=" N   LYS G  13 " --> pdb=" O   ALA G   9 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   ASP G  21 " --> pdb=" O   ASP G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 57
      No H-bonds generated for 'chain 'G' and resid 55 through 57'
    Processing helix  chain 'G' and resid 72 through 80
    Processing helix  chain 'G' and resid 141 through 152
    Processing helix  chain 'G' and resid 209 through 217
    Processing helix  chain 'G' and resid 218 through 221
    Processing helix  chain 'H' and resid 9 through 18
      removed outlier: 3.633A  pdb=" N   LYS H  13 " --> pdb=" O   ALA H   9 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 72 through 80
    Processing helix  chain 'H' and resid 141 through 152
    Processing helix  chain 'H' and resid 190 through 194
    Processing helix  chain 'H' and resid 209 through 216
    Processing helix  chain 'H' and resid 217 through 219
      No H-bonds generated for 'chain 'H' and resid 217 through 219'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228
      removed outlier: 3.749A  pdb=" N   VAL A 227 " --> pdb=" O   GLU A 483 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 362 through 365
      removed outlier: 3.664A  pdb=" N   CYS A 438 " --> pdb=" O   LEU A 336 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   ILE A 335 " --> pdb=" O   PHE A 459 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   THR A 461 " --> pdb=" O   ILE A 335 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   HIS A 337 " --> pdb=" O   THR A 461 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 600 through 601
      removed outlier: 6.411A  pdb=" N   LEU A 600 " --> pdb=" O   VAL E  76 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 77
      removed outlier: 6.033A  pdb=" N   LYS B 109 " --> pdb=" O   ARG B 139 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   ALA B 141 " --> pdb=" O   LYS B 109 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   VAL B 111 " --> pdb=" O   ALA B 141 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   ALA B 143 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   LEU B 113 " --> pdb=" O   ALA B 143 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   MET B  45 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   CYS B 144 " --> pdb=" O   MET B  45 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ILE B  47 " --> pdb=" O   CYS B 144 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 49 through 52
      removed outlier: 6.281A  pdb=" N   LEU C  50 " --> pdb=" O   PHE C 164 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 79 through 83
      removed outlier: 6.116A  pdb=" N   LYS C 112 " --> pdb=" O   ARG C 142 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 64
    Processing sheet with id=AA8, first strand: chain 'D' and resid 135 through 140
      removed outlier: 5.544A  pdb=" N   LYS D 135 " --> pdb=" O   ARG D 165 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   CYS D 167 " --> pdb=" O   LYS D 135 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   ILE D 137 " --> pdb=" O   CYS D 167 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   ILE D 169 " --> pdb=" O   ILE D 137 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   LEU D 139 " --> pdb=" O   ILE D 169 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'E' and resid 93 through 96
      removed outlier: 6.498A  pdb=" N   LEU E  94 " --> pdb=" O   ILE E 139 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   ASN E 141 " --> pdb=" O   LEU E  94 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   ILE E  96 " --> pdb=" O   ASN E 141 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   LYS E 136 " --> pdb=" O   ARG E 166 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   ILE E 168 " --> pdb=" O   LYS E 136 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   VAL E 138 " --> pdb=" O   ILE E 168 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   VAL E 170 " --> pdb=" O   VAL E 138 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ILE E 140 " --> pdb=" O   VAL E 170 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LEU E  39 " --> pdb=" O   MET E 169 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   CYS E 171 " --> pdb=" O   LEU E  39 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   LEU E  41 " --> pdb=" O   CYS E 171 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 57 through 60
      removed outlier: 3.597A  pdb=" N   GLU F  59 " --> pdb=" O   LYS F   5 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   LEU F  88 " --> pdb=" O   PHE F   6 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 71
      removed outlier: 3.751A  pdb=" N   MET F  70 " --> pdb=" O   VAL F  26 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   VAL F  26 " --> pdb=" O   MET F  70 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   LEU F  25 " --> pdb=" O   VAL F  40 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   VAL F  40 " --> pdb=" O   LEU F  25 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ASN F  27 " --> pdb=" O   GLN F  38 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLN F  38 " --> pdb=" O   ASN F  27 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU F 250 " --> pdb=" O   ALA F 235 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   ASP F 240 " --> pdb=" O   ARG F 224 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   ARG F 224 " --> pdb=" O   ASP F 240 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   THR F 136 " --> pdb=" O   GLU F 198 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LYS F 196 " --> pdb=" O   SER F 138 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 204 through 208
      removed outlier: 3.759A  pdb=" N   LEU F 205 " --> pdb=" O   ILE F 160 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   SER F 157 " --> pdb=" O   ASP F 172 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   ASP F 172 " --> pdb=" O   SER F 157 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA F 171 " --> pdb=" O   GLY F 178 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLY F 178 " --> pdb=" O   ALA F 171 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER F 177 " --> pdb=" O   SER G 115 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   SER F 179 " --> pdb=" O   GLU G 113 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   GLU G 113 " --> pdb=" O   SER F 179 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ILE G 100 " --> pdb=" O   ILE G  91 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU G   2 " --> pdb=" O   ALA G  92 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71
      removed outlier: 3.792A  pdb=" N   MET G  70 " --> pdb=" O   VAL G  26 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   VAL G  26 " --> pdb=" O   MET G  70 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   LEU G  25 " --> pdb=" O   VAL G  40 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   VAL G  40 " --> pdb=" O   LEU G  25 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   ASN G  27 " --> pdb=" O   GLN G  38 " (cutoff:3.500A)
      removed outlier: 5.002A  pdb=" N   GLN G  38 " --> pdb=" O   ASN G  27 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ASP G 240 " --> pdb=" O   ARG G 224 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ARG G 224 " --> pdb=" O   ASP G 240 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'G' and resid 206 through 208
      removed outlier: 6.028A  pdb=" N   SER G 157 " --> pdb=" O   ASP G 172 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   ASP G 172 " --> pdb=" O   SER G 157 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ILE G 181 " --> pdb=" O   ILE H 111 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ILE H 111 " --> pdb=" O   ILE G 181 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   LEU H  88 " --> pdb=" O   PHE H   6 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLU H  59 " --> pdb=" O   LYS H   5 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 71
      removed outlier: 5.936A  pdb=" N   LEU H  25 " --> pdb=" O   VAL H  40 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   VAL H  40 " --> pdb=" O   LEU H  25 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ASN H  27 " --> pdb=" O   GLN H  38 " (cutoff:3.500A)
      removed outlier: 5.054A  pdb=" N   SER H 230 " --> pdb=" O   PRO H 234 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   ASP H 240 " --> pdb=" O   ARG H 224 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   ARG H 224 " --> pdb=" O   ASP H 240 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU H 139 " --> pdb=" O   VAL H 225 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 177 through 182
      removed outlier: 3.548A  pdb=" N   GLY H 178 " --> pdb=" O   ALA H 171 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA H 171 " --> pdb=" O   GLY H 178 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   ASP H 172 " --> pdb=" O   SER H 157 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   SER H 157 " --> pdb=" O   ASP H 172 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   LEU H 205 " --> pdb=" O   ILE H 160 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ILE H 162 " --> pdb=" O   VAL H 203 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   VAL H 203 " --> pdb=" O   ILE H 162 " (cutoff:3.500A)

    1047 hydrogen bonds defined for protein.
    3015 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: 8.54

  Time building geometry restraints manager: 6.64 seconds

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

  Histogram of bond lengths:
        1.21 -     1.36: 6749
        1.36 -     1.51: 5016
        1.51 -     1.65: 8806
        1.65 -     1.80: 75
        1.80 -     1.95: 77
  Bond restraints: 20723
  Sorted by residual:
  bond pdb=" C   PRO D 132 "
       pdb=" O   PRO D 132 "
    ideal  model  delta    sigma   weight residual
    1.246  1.213  0.033 8.50e-03 1.38e+04 1.47e+01
  bond pdb=" CA  PRO D 132 "
       pdb=" C   PRO D 132 "
    ideal  model  delta    sigma   weight residual
    1.514  1.534 -0.019 5.50e-03 3.31e+04 1.23e+01
  bond pdb=" N   ARG D 101 "
       pdb=" CA  ARG D 101 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.035 1.21e-02 6.83e+03 8.55e+00
  bond pdb=" N   GLY C 110 "
       pdb=" CA  GLY C 110 "
    ideal  model  delta    sigma   weight residual
    1.450  1.476 -0.026 9.10e-03 1.21e+04 8.11e+00
  bond pdb=" N   ILE E  96 "
       pdb=" CA  ILE E  96 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.24e-02 6.50e+03 8.05e+00
  ... (remaining 20718 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 27441
        1.96 -     3.92: 503
        3.92 -     5.88: 76
        5.88 -     7.83: 13
        7.83 -     9.79: 5
  Bond angle restraints: 28038
  Sorted by residual:
  angle pdb=" CA  ILE E  96 "
        pdb=" C   ILE E  96 "
        pdb=" O   ILE E  96 "
      ideal   model   delta    sigma   weight residual
     121.64  117.90    3.74 9.80e-01 1.04e+00 1.46e+01
  angle pdb=" N   ILE F 128 "
        pdb=" CA  ILE F 128 "
        pdb=" C   ILE F 128 "
      ideal   model   delta    sigma   weight residual
     111.91  108.62    3.29 8.90e-01 1.26e+00 1.37e+01
  angle pdb=" N   LYS G  20 "
        pdb=" CA  LYS G  20 "
        pdb=" C   LYS G  20 "
      ideal   model   delta    sigma   weight residual
     111.02  115.53   -4.51 1.22e+00 6.72e-01 1.37e+01
  angle pdb=" CA  CYS H  81 "
        pdb=" C   CYS H  81 "
        pdb=" O   CYS H  81 "
      ideal   model   delta    sigma   weight residual
     122.63  117.87    4.76 1.29e+00 6.01e-01 1.36e+01
  angle pdb=" C   GLN E  32 "
        pdb=" CA  GLN E  32 "
        pdb=" CB  GLN E  32 "
      ideal   model   delta    sigma   weight residual
     110.33  113.95   -3.62 1.02e+00 9.61e-01 1.26e+01
  ... (remaining 28033 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.07: 11840
       25.07 -    50.14: 812
       50.14 -    75.21: 133
       75.21 -   100.28: 8
      100.28 -   125.35: 1
  Dihedral angle restraints: 12794
    sinusoidal: 5292
      harmonic: 7502
  Sorted by residual:
  dihedral pdb=" O1B ADP E 401 "
           pdb=" O3A ADP E 401 "
           pdb=" PB  ADP E 401 "
           pdb=" PA  ADP E 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  174.65  125.35     1      2.00e+01 2.50e-03 3.79e+01
  dihedral pdb=" CA  LEU D  58 "
           pdb=" C   LEU D  58 "
           pdb=" N   PRO D  59 "
           pdb=" CA  PRO D  59 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.47   19.53     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  PHE C 331 "
           pdb=" C   PHE C 331 "
           pdb=" N   GLU C 332 "
           pdb=" CA  GLU C 332 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.58   18.42     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 12791 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 2729
       0.054 -    0.107: 477
       0.107 -    0.161: 77
       0.161 -    0.215: 7
       0.215 -    0.268: 1
  Chirality restraints: 3291
  Sorted by residual:
  chirality pdb=" CB  ILE F 162 "
            pdb=" CA  ILE F 162 "
            pdb=" CG1 ILE F 162 "
            pdb=" CG2 ILE F 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.91   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  ILE E  96 "
            pdb=" N   ILE E  96 "
            pdb=" C   ILE E  96 "
            pdb=" CB  ILE E  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  ILE C 106 "
            pdb=" N   ILE C 106 "
            pdb=" C   ILE C 106 "
            pdb=" CB  ILE C 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 3288 not shown)

  Planarity restraints: 3551
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D  66 "    0.060 5.00e-02 4.00e+02   9.03e-02 1.31e+01
        pdb=" N   PRO D  67 "   -0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO D  67 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO D  67 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 196 "   -0.044 5.00e-02 4.00e+02   6.40e-02 6.56e+00
        pdb=" N   PRO A 197 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 197 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 197 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS C 144 "    0.012 2.00e-02 2.50e+03   2.41e-02 5.82e+00
        pdb=" C   CYS C 144 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   CYS C 144 "    0.016 2.00e-02 2.50e+03
        pdb=" N   VAL C 145 "    0.014 2.00e-02 2.50e+03
  ... (remaining 3548 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 301
        2.67 -     3.22: 19112
        3.22 -     3.78: 31860
        3.78 -     4.34: 43124
        4.34 -     4.90: 71679
  Nonbonded interactions: 166076
  Sorted by model distance:
  nonbonded pdb=" O   GLY D  70 "
            pdb=" OG1 THR D  74 "
     model   vdw
     2.107 3.040
  nonbonded pdb=" OG1 THR B  56 "
            pdb="MG    MG B 402 "
     model   vdw
     2.142 2.170
  nonbonded pdb=" OD2 ASP D 140 "
            pdb="MG    MG D 402 "
     model   vdw
     2.210 2.170
  nonbonded pdb=" O   LYS F  31 "
            pdb=" OH  TYR F  60 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O2B AGS D 401 "
            pdb="MG    MG D 402 "
     model   vdw
     2.255 2.170
  ... (remaining 166071 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'F'
  selection = (chain 'G' and resid 1 through 254)
  selection = (chain 'H' and resid 1 through 254)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.890
  Check model and map are aligned:         0.160
  Set scattering table:                    0.210
  Process input model:                     51.640
  Find NCS groups from input model:        0.550
  Set up NCS constraints:                  0.090
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   61.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
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      :  0.003   0.099  20723  Z= 0.185
  Angle     :  0.652   9.794  28038  Z= 0.370
  Chirality :  0.042   0.268   3291
  Planarity :  0.005   0.090   3551
  Dihedral  : 16.149 125.349   7896
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 18.06 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.16), residues: 2527
  helix:  1.22 (0.15), residues: 1144
  sheet:  0.11 (0.25), residues: 471
  loop : -1.28 (0.19), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 488 
 HIS   0.004   0.001   HIS D 124 
 PHE   0.025   0.001   PHE A 509 
 TYR   0.016   0.001   TYR D  64 
 ARG   0.010   0.001   ARG G 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17325 ( 1047)
  hydrogen bonds       : angle       6.77174 ( 3015)
  covalent geometry    : bond        0.00312 (20723)
  covalent geometry    : angle       0.65205 (28038)

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

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

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  663 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 653
  time to evaluate  : 2.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  224 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6581 (tp40)
REVERT: A  359 ASN cc_start: 0.7637 (p0) cc_final: 0.7185 (t0)
REVERT: A  361 TYR cc_start: 0.8663 (p90) cc_final: 0.8170 (p90)
REVERT: A  505 MET cc_start: 0.8954 (tpp) cc_final: 0.8424 (mmt)
REVERT: A  588 MET cc_start: 0.7567 (mmp) cc_final: 0.6882 (mtm)
REVERT: C   15 TRP cc_start: 0.8650 (m-10) cc_final: 0.8228 (m-10)
REVERT: C   30 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7671 (mm-40)
REVERT: C  109 LYS cc_start: 0.6744 (OUTLIER) cc_final: 0.6031 (mptt)
REVERT: D   49 LEU cc_start: 0.8525 (mt) cc_final: 0.8256 (mt)
REVERT: D   83 TYR cc_start: 0.5684 (m-10) cc_final: 0.5181 (m-10)
REVERT: D  132 PRO cc_start: 0.7948 (Cg_exo) cc_final: 0.7743 (Cg_endo)
REVERT: D  134 TYR cc_start: 0.5532 (p90) cc_final: 0.5141 (p90)
REVERT: D  343 LEU cc_start: 0.8749 (tp) cc_final: 0.8323 (tp)
REVERT: F   70 MET cc_start: 0.1808 (mtp) cc_final: 0.1353 (mtp)
REVERT: F  137 LEU cc_start: 0.1989 (pp) cc_final: 0.1704 (pp)
REVERT: F  180 VAL cc_start: 0.2749 (t) cc_final: 0.2439 (m)
REVERT: F  196 LYS cc_start: 0.3868 (mmtt) cc_final: 0.3565 (tptp)
REVERT: G    8 GLU cc_start: 0.5159 (tp30) cc_final: 0.4905 (tm-30)
REVERT: G   36 ILE cc_start: 0.6974 (pt) cc_final: 0.6737 (mt)
REVERT: G   63 ASP cc_start: 0.4360 (p0) cc_final: 0.4106 (p0)
REVERT: H    7 GLU cc_start: 0.6904 (mp0) cc_final: 0.6518 (tt0)
REVERT: H   58 GLN cc_start: 0.7925 (tt0) cc_final: 0.7479 (mt0)
REVERT: H  124 ASP cc_start: 0.6315 (t70) cc_final: 0.4742 (p0)
REVERT: H  196 LYS cc_start: 0.6118 (mmtm) cc_final: 0.5839 (ttpt)
  outliers start: 10
  outliers final: 2
  residues processed: 660
  average time/residue: 0.3589
  time to fit residues: 351.5574
Evaluate side-chains
  365 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 361
  time to evaluate  : 2.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  109 LYS
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 211 optimal weight:   10.0000
   chunk 190 optimal weight:   20.0000
   chunk 105 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 128 optimal weight:    0.2980
   chunk 101 optimal weight:    1.9990
   chunk 196 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9990
   chunk 119 optimal weight:    3.9990
   chunk 146 optimal weight:    0.7980
   chunk 227 optimal weight:    2.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 243 GLN
A 406 ASN
** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 496 ASN
** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 108 HIS
B 220 ASN
D  42 GLN
D 313 ASN
E  32 GLN
G  94 ASN
G 153 GLN
** H  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 153 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.188653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.126399 restraints weight = 28037.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.46
r_work: 0.3410 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  20723  Z= 0.195
  Angle     :  0.656  10.707  28038  Z= 0.329
  Chirality :  0.044   0.225   3291
  Planarity :  0.005   0.054   3551
  Dihedral  :  7.558 115.719   2825
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 17.98 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.16), residues: 2527
  helix:  1.39 (0.15), residues: 1152
  sheet:  0.07 (0.25), residues: 455
  loop : -1.07 (0.19), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 420 
 HIS   0.004   0.001   HIS G 190 
 PHE   0.027   0.002   PHE A 509 
 TYR   0.020   0.002   TYR D 160 
 ARG   0.012   0.001   ARG E  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04516 ( 1047)
  hydrogen bonds       : angle       5.06847 ( 3015)
  covalent geometry    : bond        0.00455 (20723)
  covalent geometry    : angle       0.65595 (28038)

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

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

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  477 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 386
  time to evaluate  : 2.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  224 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6833 (tp40)
REVERT: A  359 ASN cc_start: 0.7610 (p0) cc_final: 0.7224 (t0)
REVERT: A  361 TYR cc_start: 0.8970 (p90) cc_final: 0.8531 (p90)
REVERT: A  505 MET cc_start: 0.9022 (tpp) cc_final: 0.8452 (mmt)
REVERT: A  588 MET cc_start: 0.7491 (mmp) cc_final: 0.6741 (mtm)
REVERT: B  115 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8119 (mt-10)
REVERT: C  109 LYS cc_start: 0.6688 (OUTLIER) cc_final: 0.5839 (mptt)
REVERT: C  139 LYS cc_start: 0.8907 (tppt) cc_final: 0.8589 (mptt)
REVERT: C  140 ASN cc_start: 0.7988 (t0) cc_final: 0.7707 (t0)
REVERT: C  316 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7760 (t0)
REVERT: D  132 PRO cc_start: 0.8052 (Cg_exo) cc_final: 0.7824 (Cg_endo)
REVERT: D  157 MET cc_start: 0.7171 (ptt) cc_final: 0.6618 (ptt)
REVERT: D  249 LYS cc_start: 0.8548 (mttt) cc_final: 0.8051 (mtpt)
REVERT: E    8 TYR cc_start: 0.8277 (m-80) cc_final: 0.7729 (m-10)
REVERT: E  217 ASP cc_start: 0.8015 (t0) cc_final: 0.7747 (t0)
REVERT: F   70 MET cc_start: 0.2042 (mtp) cc_final: 0.1540 (mtp)
REVERT: F  174 ASP cc_start: 0.6555 (p0) cc_final: 0.6266 (m-30)
REVERT: F  196 LYS cc_start: 0.4270 (mmtt) cc_final: 0.3818 (tptp)
REVERT: F  249 PHE cc_start: 0.5518 (m-80) cc_final: 0.3891 (m-80)
REVERT: G    1 MET cc_start: 0.3232 (mtt) cc_final: 0.2946 (mtt)
REVERT: G    8 GLU cc_start: 0.5767 (tp30) cc_final: 0.5178 (tm-30)
REVERT: G   63 ASP cc_start: 0.5316 (p0) cc_final: 0.5002 (p0)
REVERT: G  190 HIS cc_start: 0.4870 (p90) cc_final: 0.4578 (p-80)
REVERT: H    7 GLU cc_start: 0.7425 (mp0) cc_final: 0.6793 (tt0)
REVERT: H   24 GLN cc_start: 0.8069 (tt0) cc_final: 0.7763 (mt0)
REVERT: H   58 GLN cc_start: 0.8024 (tt0) cc_final: 0.7583 (mt0)
REVERT: H  146 LYS cc_start: 0.8094 (tptm) cc_final: 0.7854 (tptm)
REVERT: H  196 LYS cc_start: 0.5396 (mmtm) cc_final: 0.4852 (ttmm)
REVERT: H  245 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6913 (p90)
  outliers start: 91
  outliers final: 42
  residues processed: 451
  average time/residue: 0.3146
  time to fit residues: 220.6384
Evaluate side-chains
  365 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 319
  time to evaluate  : 2.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  372 ARG
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain C residue   73 LYS
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain C residue  109 LYS
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   63 PHE
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain E residue   12 SER
Chi-restraints excluded: chain E residue   89 SER
Chi-restraints excluded: chain E residue   93 HIS
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  206 VAL
Chi-restraints excluded: chain E residue  208 ASN
Chi-restraints excluded: chain F residue   28 PHE
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue  119 MET
Chi-restraints excluded: chain F residue  181 ILE
Chi-restraints excluded: chain F residue  203 VAL
Chi-restraints excluded: chain F residue  246 LEU
Chi-restraints excluded: chain G residue    3 GLU
Chi-restraints excluded: chain G residue   28 PHE
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue  206 THR
Chi-restraints excluded: chain H residue   67 THR
Chi-restraints excluded: chain H residue   95 THR
Chi-restraints excluded: chain H residue  113 GLU
Chi-restraints excluded: chain H residue  139 LEU
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain H residue  225 VAL
Chi-restraints excluded: chain H residue  245 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 171 optimal weight:    2.9990
   chunk 157 optimal weight:    7.9990
   chunk 133 optimal weight:    1.9990
   chunk 156 optimal weight:    2.9990
   chunk 163 optimal weight:    3.9990
   chunk 99 optimal weight:    0.0970
   chunk 66 optimal weight:    0.8980
   chunk 232 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 121 optimal weight:    0.3980
   chunk 190 optimal weight:    0.0980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 406 ASN
** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 711 GLN
B  41 ASN
C 140 ASN
** D  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 313 ASN
E  18 HIS
E 317 ASN
H  29 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.189197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.127797 restraints weight = 27779.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 2.42
r_work: 0.3440 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  20723  Z= 0.129
  Angle     :  0.568   9.585  28038  Z= 0.284
  Chirality :  0.041   0.206   3291
  Planarity :  0.004   0.041   3551
  Dihedral  :  7.334 115.437   2821
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 19.24 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.17), residues: 2527
  helix:  1.58 (0.15), residues: 1158
  sheet:  0.12 (0.24), residues: 458
  loop : -0.94 (0.19), residues: 911

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  11 
 HIS   0.003   0.001   HIS A 506 
 PHE   0.022   0.001   PHE A 509 
 TYR   0.016   0.001   TYR E   8 
 ARG   0.005   0.000   ARG H  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03843 ( 1047)
  hydrogen bonds       : angle       4.74501 ( 3015)
  covalent geometry    : bond        0.00294 (20723)
  covalent geometry    : angle       0.56793 (28038)

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

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

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  429 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 351
  time to evaluate  : 2.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  359 ASN cc_start: 0.7579 (p0) cc_final: 0.7231 (t0)
REVERT: A  361 TYR cc_start: 0.8932 (p90) cc_final: 0.8628 (p90)
REVERT: A  505 MET cc_start: 0.8907 (tpp) cc_final: 0.8327 (mmt)
REVERT: A  528 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6194 (tp)
REVERT: A  588 MET cc_start: 0.7495 (mmp) cc_final: 0.6755 (mtm)
REVERT: B  115 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8075 (mt-10)
REVERT: B  199 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7268 (mm-30)
REVERT: C   99 ASP cc_start: 0.8616 (m-30) cc_final: 0.8353 (m-30)
REVERT: C  109 LYS cc_start: 0.6639 (OUTLIER) cc_final: 0.5779 (mptt)
REVERT: C  139 LYS cc_start: 0.8775 (tppt) cc_final: 0.8532 (mptt)
REVERT: C  316 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7615 (t0)
REVERT: D  131 CYS cc_start: 0.8191 (p) cc_final: 0.6861 (t)
REVERT: D  188 ARG cc_start: 0.6794 (ttt-90) cc_final: 0.6429 (ttt-90)
REVERT: E   67 ARG cc_start: 0.8168 (mtp-110) cc_final: 0.7845 (mtt90)
REVERT: E  100 ASP cc_start: 0.7615 (t0) cc_final: 0.7395 (t0)
REVERT: F  126 LEU cc_start: 0.3000 (mt) cc_final: 0.2624 (tp)
REVERT: F  174 ASP cc_start: 0.6598 (p0) cc_final: 0.6343 (m-30)
REVERT: F  196 LYS cc_start: 0.4305 (mmtt) cc_final: 0.3838 (tptp)
REVERT: F  249 PHE cc_start: 0.5417 (m-80) cc_final: 0.3904 (m-80)
REVERT: G    1 MET cc_start: 0.3195 (mtt) cc_final: 0.2970 (mtt)
REVERT: G   63 ASP cc_start: 0.5349 (p0) cc_final: 0.5112 (p0)
REVERT: G  190 HIS cc_start: 0.4955 (p90) cc_final: 0.4666 (p-80)
REVERT: H    7 GLU cc_start: 0.7388 (mp0) cc_final: 0.6821 (tt0)
REVERT: H   24 GLN cc_start: 0.8146 (tt0) cc_final: 0.7845 (mt0)
REVERT: H   44 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7990 (mtt180)
REVERT: H   58 GLN cc_start: 0.8004 (tt0) cc_final: 0.7690 (mt0)
REVERT: H  196 LYS cc_start: 0.5278 (mmtm) cc_final: 0.4892 (ttmm)
REVERT: H  245 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6878 (p90)
  outliers start: 78
  outliers final: 47
  residues processed: 407
  average time/residue: 0.3153
  time to fit residues: 199.6410
Evaluate side-chains
  364 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 313
  time to evaluate  : 2.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  558 ASN
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  109 LYS
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   63 PHE
Chi-restraints excluded: chain D residue  164 THR
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain E residue   12 SER
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  206 VAL
Chi-restraints excluded: chain E residue  208 ASN
Chi-restraints excluded: chain E residue  254 ILE
Chi-restraints excluded: chain E residue  333 SER
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue  119 MET
Chi-restraints excluded: chain F residue  188 MET
Chi-restraints excluded: chain F residue  203 VAL
Chi-restraints excluded: chain F residue  246 LEU
Chi-restraints excluded: chain G residue    3 GLU
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   36 ILE
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue  181 ILE
Chi-restraints excluded: chain G residue  206 THR
Chi-restraints excluded: chain H residue  139 LEU
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain H residue  225 VAL
Chi-restraints excluded: chain H residue  245 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 108 optimal weight:    1.9990
   chunk 208 optimal weight:    9.9990
   chunk 167 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 233 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 123 optimal weight:    3.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 549 ASN
A 622 GLN
B 250 GLN
D  25 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.181484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.133530 restraints weight = 28034.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 2.76
r_work: 0.3270 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.4050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  20723  Z= 0.193
  Angle     :  0.598  10.012  28038  Z= 0.299
  Chirality :  0.043   0.215   3291
  Planarity :  0.004   0.040   3551
  Dihedral  :  7.312 116.487   2818
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 19.63 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.17), residues: 2527
  helix:  1.49 (0.15), residues: 1159
  sheet:  0.07 (0.24), residues: 460
  loop : -0.91 (0.19), residues: 908

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 780 
 HIS   0.004   0.001   HIS B 232 
 PHE   0.020   0.002   PHE A 509 
 TYR   0.016   0.002   TYR D 286 
 ARG   0.007   0.001   ARG H  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04067 ( 1047)
  hydrogen bonds       : angle       4.63556 ( 3015)
  covalent geometry    : bond        0.00465 (20723)
  covalent geometry    : angle       0.59848 (28038)

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

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

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  418 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 328
  time to evaluate  : 2.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  361 TYR cc_start: 0.8969 (p90) cc_final: 0.8704 (p90)
REVERT: A  505 MET cc_start: 0.8778 (tpp) cc_final: 0.8221 (mmt)
REVERT: A  528 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6171 (tp)
REVERT: A  588 MET cc_start: 0.7662 (mmp) cc_final: 0.6985 (mtm)
REVERT: B   94 LYS cc_start: 0.9073 (ttpp) cc_final: 0.8866 (tttp)
REVERT: B  204 GLN cc_start: 0.8741 (tp-100) cc_final: 0.8479 (tp-100)
REVERT: C  109 LYS cc_start: 0.6560 (OUTLIER) cc_final: 0.5793 (mptt)
REVERT: C  139 LYS cc_start: 0.8811 (tppt) cc_final: 0.8574 (mptt)
REVERT: C  316 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7722 (t0)
REVERT: D   81 GLU cc_start: 0.7650 (tt0) cc_final: 0.7282 (mt-10)
REVERT: D  131 CYS cc_start: 0.8288 (p) cc_final: 0.7159 (t)
REVERT: D  188 ARG cc_start: 0.6918 (ttt-90) cc_final: 0.6696 (ttt-90)
REVERT: E  224 GLN cc_start: 0.8805 (tt0) cc_final: 0.8444 (mt0)
REVERT: E  249 LYS cc_start: 0.7724 (mtpp) cc_final: 0.7167 (mmmt)
REVERT: F   50 LEU cc_start: 0.8019 (pp) cc_final: 0.7563 (mt)
REVERT: F  126 LEU cc_start: 0.3139 (mt) cc_final: 0.2732 (tp)
REVERT: F  174 ASP cc_start: 0.6626 (p0) cc_final: 0.6354 (m-30)
REVERT: F  196 LYS cc_start: 0.4348 (mmtt) cc_final: 0.3890 (tptp)
REVERT: F  246 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.6917 (tt)
REVERT: F  249 PHE cc_start: 0.5391 (m-80) cc_final: 0.3799 (m-80)
REVERT: G    1 MET cc_start: 0.3436 (mtt) cc_final: 0.3233 (mtt)
REVERT: G   63 ASP cc_start: 0.5370 (p0) cc_final: 0.5151 (p0)
REVERT: G  190 HIS cc_start: 0.5145 (p90) cc_final: 0.4814 (p-80)
REVERT: H    7 GLU cc_start: 0.7505 (mp0) cc_final: 0.6567 (pm20)
REVERT: H   24 GLN cc_start: 0.8207 (tt0) cc_final: 0.7969 (mt0)
REVERT: H   44 ARG cc_start: 0.8398 (mtt90) cc_final: 0.8157 (mtt180)
REVERT: H   58 GLN cc_start: 0.8051 (tt0) cc_final: 0.7706 (mt0)
REVERT: H   80 ARG cc_start: 0.7821 (ttp-110) cc_final: 0.7416 (mtm110)
REVERT: H  196 LYS cc_start: 0.5628 (mmtm) cc_final: 0.5094 (ttmm)
REVERT: H  245 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7294 (p90)
  outliers start: 90
  outliers final: 56
  residues processed: 394
  average time/residue: 0.3119
  time to fit residues: 190.2627
Evaluate side-chains
  360 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 299
  time to evaluate  : 2.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  372 ARG
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  558 ASN
Chi-restraints excluded: chain A residue  596 ILE
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  109 LYS
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  202 ASN
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain D residue  266 ASP
Chi-restraints excluded: chain E residue   12 SER
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   89 SER
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  206 VAL
Chi-restraints excluded: chain E residue  246 LEU
Chi-restraints excluded: chain E residue  251 SER
Chi-restraints excluded: chain E residue  333 SER
Chi-restraints excluded: chain F residue   28 PHE
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue  188 MET
Chi-restraints excluded: chain F residue  246 LEU
Chi-restraints excluded: chain G residue    2 LEU
Chi-restraints excluded: chain G residue    3 GLU
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   73 THR
Chi-restraints excluded: chain G residue  181 ILE
Chi-restraints excluded: chain G residue  206 THR
Chi-restraints excluded: chain G residue  221 LEU
Chi-restraints excluded: chain H residue   46 LEU
Chi-restraints excluded: chain H residue   67 THR
Chi-restraints excluded: chain H residue   95 THR
Chi-restraints excluded: chain H residue  111 ILE
Chi-restraints excluded: chain H residue  139 LEU
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain H residue  225 VAL
Chi-restraints excluded: chain H residue  245 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 118 optimal weight:    0.0980
   chunk 99 optimal weight:    7.9990
   chunk 208 optimal weight:    7.9990
   chunk 217 optimal weight:    4.9990
   chunk 215 optimal weight:    1.9990
   chunk 138 optimal weight:    0.6980
   chunk 172 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 406 ASN
** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 711 GLN
D  25 GLN
** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  32 GLN
E 104 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.188063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.137417 restraints weight = 28191.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 2.88
r_work: 0.3351 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  20723  Z= 0.115
  Angle     :  0.541  11.427  28038  Z= 0.268
  Chirality :  0.040   0.214   3291
  Planarity :  0.003   0.032   3551
  Dihedral  :  7.163 115.060   2818
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 21.32 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.17), residues: 2527
  helix:  1.72 (0.15), residues: 1155
  sheet:  0.05 (0.24), residues: 475
  loop : -0.77 (0.20), residues: 897

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 266 
 HIS   0.004   0.001   HIS A 272 
 PHE   0.023   0.001   PHE G  19 
 TYR   0.020   0.001   TYR H 211 
 ARG   0.005   0.000   ARG D 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03459 ( 1047)
  hydrogen bonds       : angle       4.43560 ( 3015)
  covalent geometry    : bond        0.00264 (20723)
  covalent geometry    : angle       0.54094 (28038)

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

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

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  411 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 332
  time to evaluate  : 2.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ARG cc_start: 0.8062 (mmt-90) cc_final: 0.7770 (mmt-90)
REVERT: A  361 TYR cc_start: 0.8946 (p90) cc_final: 0.8735 (p90)
REVERT: A  505 MET cc_start: 0.8693 (tpp) cc_final: 0.8214 (mmt)
REVERT: A  588 MET cc_start: 0.7536 (mmp) cc_final: 0.6872 (mtm)
REVERT: C  109 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.5819 (mptt)
REVERT: C  316 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7567 (t0)
REVERT: D   81 GLU cc_start: 0.7683 (tt0) cc_final: 0.7200 (mt-10)
REVERT: D  188 ARG cc_start: 0.6938 (ttt-90) cc_final: 0.6719 (ttt-90)
REVERT: E    8 TYR cc_start: 0.8205 (m-80) cc_final: 0.7726 (m-10)
REVERT: E   67 ARG cc_start: 0.8295 (mtp-110) cc_final: 0.8094 (mtt90)
REVERT: E  101 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7127 (ptt)
REVERT: E  224 GLN cc_start: 0.8758 (tt0) cc_final: 0.8441 (mt0)
REVERT: F  126 LEU cc_start: 0.3091 (mt) cc_final: 0.2698 (tp)
REVERT: F  174 ASP cc_start: 0.6585 (p0) cc_final: 0.6303 (m-30)
REVERT: F  196 LYS cc_start: 0.4372 (mmtt) cc_final: 0.3912 (tptp)
REVERT: F  246 LEU cc_start: 0.7579 (tt) cc_final: 0.7305 (tt)
REVERT: F  249 PHE cc_start: 0.5333 (m-80) cc_final: 0.3805 (m-80)
REVERT: G    1 MET cc_start: 0.3428 (mtt) cc_final: 0.3017 (mtt)
REVERT: G  125 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5831 (t80)
REVERT: G  190 HIS cc_start: 0.4996 (p90) cc_final: 0.4791 (p90)
REVERT: H    7 GLU cc_start: 0.7464 (mp0) cc_final: 0.6607 (pm20)
REVERT: H   24 GLN cc_start: 0.8266 (tt0) cc_final: 0.7990 (mt0)
REVERT: H   58 GLN cc_start: 0.7963 (tt0) cc_final: 0.7659 (mt0)
REVERT: H   80 ARG cc_start: 0.7874 (ttp-110) cc_final: 0.7514 (mtm110)
REVERT: H  122 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.7088 (p0)
REVERT: H  124 ASP cc_start: 0.6810 (t70) cc_final: 0.5502 (p0)
REVERT: H  196 LYS cc_start: 0.5582 (mmtm) cc_final: 0.5020 (ttmm)
REVERT: H  245 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.7189 (p90)
  outliers start: 79
  outliers final: 51
  residues processed: 388
  average time/residue: 0.3364
  time to fit residues: 200.8968
Evaluate side-chains
  362 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 305
  time to evaluate  : 2.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  558 ASN
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  109 LYS
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  202 ASN
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain D residue   25 GLN
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  266 ASP
Chi-restraints excluded: chain E residue   12 SER
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  101 MET
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  206 VAL
Chi-restraints excluded: chain E residue  246 LEU
Chi-restraints excluded: chain E residue  251 SER
Chi-restraints excluded: chain E residue  353 LEU
Chi-restraints excluded: chain F residue   28 PHE
Chi-restraints excluded: chain F residue  188 MET
Chi-restraints excluded: chain G residue    2 LEU
Chi-restraints excluded: chain G residue    3 GLU
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   97 ASP
Chi-restraints excluded: chain G residue  125 PHE
Chi-restraints excluded: chain G residue  181 ILE
Chi-restraints excluded: chain H residue   46 LEU
Chi-restraints excluded: chain H residue   95 THR
Chi-restraints excluded: chain H residue  111 ILE
Chi-restraints excluded: chain H residue  122 ASP
Chi-restraints excluded: chain H residue  139 LEU
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain H residue  225 VAL
Chi-restraints excluded: chain H residue  245 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 165 optimal weight:    3.9990
   chunk 227 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 195 optimal weight:    5.9990
   chunk 41 optimal weight:    8.9990
   chunk 69 optimal weight:    0.0050
   chunk 35 optimal weight:    4.9990
   chunk 132 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 130 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    2.2000

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

Flipped N/Q/H residues before XYZ refinement:
** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 616 ASN
B 250 GLN
C 210 ASN
** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 190 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.183212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.132576 restraints weight = 28383.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 2.91
r_work: 0.3258 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.4780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075  20723  Z= 0.246
  Angle     :  0.640  10.279  28038  Z= 0.318
  Chirality :  0.044   0.215   3291
  Planarity :  0.004   0.056   3551
  Dihedral  :  7.403 116.563   2818
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 21.15 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.17), residues: 2527
  helix:  1.47 (0.15), residues: 1159
  sheet: -0.03 (0.24), residues: 475
  loop : -0.76 (0.20), residues: 893

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 510 
 HIS   0.005   0.001   HIS B  44 
 PHE   0.040   0.002   PHE G  19 
 TYR   0.021   0.002   TYR H 211 
 ARG   0.008   0.001   ARG C  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04274 ( 1047)
  hydrogen bonds       : angle       4.58593 ( 3015)
  covalent geometry    : bond        0.00597 (20723)
  covalent geometry    : angle       0.64014 (28038)

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

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

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  423 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 101
    poor density    : 322
  time to evaluate  : 2.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ARG cc_start: 0.8081 (mmt-90) cc_final: 0.7816 (mmt-90)
REVERT: A  505 MET cc_start: 0.8834 (tpp) cc_final: 0.8317 (mmt)
REVERT: A  528 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6126 (tp)
REVERT: A  575 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8733 (tppt)
REVERT: A  588 MET cc_start: 0.7719 (mmp) cc_final: 0.7039 (mtm)
REVERT: C  109 LYS cc_start: 0.6653 (OUTLIER) cc_final: 0.5940 (mptt)
REVERT: C  316 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7760 (t0)
REVERT: D   81 GLU cc_start: 0.7632 (tt0) cc_final: 0.7147 (mt-10)
REVERT: D  131 CYS cc_start: 0.8570 (p) cc_final: 0.7513 (t)
REVERT: D  154 ARG cc_start: 0.6764 (mmm160) cc_final: 0.6556 (mmm160)
REVERT: D  188 ARG cc_start: 0.7110 (ttt-90) cc_final: 0.6876 (ttt-90)
REVERT: E  224 GLN cc_start: 0.8736 (tt0) cc_final: 0.8398 (mt0)
REVERT: E  249 LYS cc_start: 0.7773 (mtpp) cc_final: 0.7209 (mmmt)
REVERT: F  126 LEU cc_start: 0.3106 (mt) cc_final: 0.2716 (tp)
REVERT: F  174 ASP cc_start: 0.6721 (p0) cc_final: 0.6456 (m-30)
REVERT: F  196 LYS cc_start: 0.4320 (mmtt) cc_final: 0.3849 (tptp)
REVERT: F  249 PHE cc_start: 0.5397 (m-80) cc_final: 0.3733 (m-80)
REVERT: G  125 PHE cc_start: 0.6270 (OUTLIER) cc_final: 0.5935 (t80)
REVERT: H    7 GLU cc_start: 0.7739 (mp0) cc_final: 0.6851 (pm20)
REVERT: H   24 GLN cc_start: 0.8253 (tt0) cc_final: 0.7958 (mt0)
REVERT: H   55 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6775 (mp0)
REVERT: H   58 GLN cc_start: 0.8210 (tt0) cc_final: 0.7643 (mt0)
REVERT: H  122 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7039 (p0)
REVERT: H  124 ASP cc_start: 0.6990 (t70) cc_final: 0.5650 (p0)
REVERT: H  196 LYS cc_start: 0.5624 (mmtm) cc_final: 0.4985 (ttmm)
REVERT: H  245 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7381 (p90)
  outliers start: 101
  outliers final: 67
  residues processed: 398
  average time/residue: 0.3248
  time to fit residues: 199.0591
Evaluate side-chains
  365 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 290
  time to evaluate  : 2.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  372 ARG
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  558 ASN
Chi-restraints excluded: chain A residue  575 LYS
Chi-restraints excluded: chain A residue  596 ILE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  321 ASN
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  109 LYS
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  266 ASP
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain E residue   12 SER
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   89 SER
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  206 VAL
Chi-restraints excluded: chain E residue  246 LEU
Chi-restraints excluded: chain F residue   21 ASP
Chi-restraints excluded: chain F residue   28 PHE
Chi-restraints excluded: chain F residue  188 MET
Chi-restraints excluded: chain F residue  246 LEU
Chi-restraints excluded: chain G residue    2 LEU
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   73 THR
Chi-restraints excluded: chain G residue   87 THR
Chi-restraints excluded: chain G residue   97 ASP
Chi-restraints excluded: chain G residue  125 PHE
Chi-restraints excluded: chain G residue  161 MET
Chi-restraints excluded: chain G residue  181 ILE
Chi-restraints excluded: chain G residue  206 THR
Chi-restraints excluded: chain H residue   46 LEU
Chi-restraints excluded: chain H residue   55 GLU
Chi-restraints excluded: chain H residue   67 THR
Chi-restraints excluded: chain H residue   95 THR
Chi-restraints excluded: chain H residue  111 ILE
Chi-restraints excluded: chain H residue  122 ASP
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  139 LEU
Chi-restraints excluded: chain H residue  182 ILE
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain H residue  245 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 226 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 111 optimal weight:   10.0000
   chunk 129 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 165 optimal weight:    1.9990
   chunk 240 optimal weight:    7.9990
   chunk 176 optimal weight:   20.0000
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 406 ASN
** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 603 ASN
** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 190 HIS
** H  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.182511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.132476 restraints weight = 28253.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 2.87
r_work: 0.3265 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.5122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  20723  Z= 0.218
  Angle     :  0.623   9.744  28038  Z= 0.312
  Chirality :  0.043   0.253   3291
  Planarity :  0.004   0.035   3551
  Dihedral  :  7.470 115.729   2818
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 21.67 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.17), residues: 2527
  helix:  1.47 (0.15), residues: 1156
  sheet: -0.12 (0.24), residues: 478
  loop : -0.79 (0.20), residues: 893

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 266 
 HIS   0.005   0.001   HIS A 272 
 PHE   0.021   0.002   PHE A 509 
 TYR   0.018   0.002   TYR H 211 
 ARG   0.009   0.001   ARG E  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04058 ( 1047)
  hydrogen bonds       : angle       4.57126 ( 3015)
  covalent geometry    : bond        0.00526 (20723)
  covalent geometry    : angle       0.62305 (28038)

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

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

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  387 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 101
    poor density    : 286
  time to evaluate  : 2.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ARG cc_start: 0.8142 (mmt-90) cc_final: 0.7890 (mmt-90)
REVERT: A  362 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8799 (mm-40)
REVERT: A  379 ASP cc_start: 0.8000 (m-30) cc_final: 0.7744 (m-30)
REVERT: A  462 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7034 (mttt)
REVERT: A  505 MET cc_start: 0.8786 (tpp) cc_final: 0.8325 (mmt)
REVERT: A  528 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6050 (tp)
REVERT: A  588 MET cc_start: 0.7745 (mmp) cc_final: 0.7127 (mtm)
REVERT: C  109 LYS cc_start: 0.6701 (OUTLIER) cc_final: 0.5999 (mptt)
REVERT: C  316 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7680 (t0)
REVERT: D   81 GLU cc_start: 0.7619 (tt0) cc_final: 0.7031 (mt-10)
REVERT: D  131 CYS cc_start: 0.8639 (p) cc_final: 0.7518 (t)
REVERT: D  188 ARG cc_start: 0.7124 (ttt-90) cc_final: 0.6837 (ttt-90)
REVERT: E  224 GLN cc_start: 0.8742 (tt0) cc_final: 0.8400 (mt0)
REVERT: F  126 LEU cc_start: 0.3096 (mt) cc_final: 0.2718 (tp)
REVERT: F  174 ASP cc_start: 0.6774 (p0) cc_final: 0.6516 (m-30)
REVERT: F  196 LYS cc_start: 0.4235 (mmtt) cc_final: 0.3805 (tptp)
REVERT: F  249 PHE cc_start: 0.5276 (m-80) cc_final: 0.3574 (m-80)
REVERT: G    8 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6998 (mp0)
REVERT: G   19 PHE cc_start: 0.6865 (t80) cc_final: 0.6505 (t80)
REVERT: G  125 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.5987 (t80)
REVERT: G  165 GLU cc_start: 0.5811 (tp30) cc_final: 0.5392 (tm-30)
REVERT: H    7 GLU cc_start: 0.7816 (mp0) cc_final: 0.6955 (pm20)
REVERT: H   24 GLN cc_start: 0.8205 (tt0) cc_final: 0.7932 (mt0)
REVERT: H   55 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6706 (mp0)
REVERT: H   58 GLN cc_start: 0.8278 (tt0) cc_final: 0.7650 (mt0)
REVERT: H   80 ARG cc_start: 0.7827 (ttp-110) cc_final: 0.7442 (mtm110)
REVERT: H  122 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.7026 (p0)
REVERT: H  124 ASP cc_start: 0.6987 (t70) cc_final: 0.5603 (p0)
REVERT: H  224 ARG cc_start: 0.6811 (mtp85) cc_final: 0.6509 (mtp85)
REVERT: H  245 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7537 (p90)
  outliers start: 101
  outliers final: 75
  residues processed: 366
  average time/residue: 0.3055
  time to fit residues: 173.8880
Evaluate side-chains
  353 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 269
  time to evaluate  : 2.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  362 GLN
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  372 ARG
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  558 ASN
Chi-restraints excluded: chain A residue  596 ILE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  109 LYS
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  164 THR
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  266 ASP
Chi-restraints excluded: chain D residue  330 ASP
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain E residue   12 SER
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   89 SER
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain E residue  109 ILE
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  206 VAL
Chi-restraints excluded: chain E residue  246 LEU
Chi-restraints excluded: chain E residue  251 SER
Chi-restraints excluded: chain E residue  333 SER
Chi-restraints excluded: chain E residue  353 LEU
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   21 ASP
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue  181 ILE
Chi-restraints excluded: chain F residue  188 MET
Chi-restraints excluded: chain G residue    2 LEU
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   73 THR
Chi-restraints excluded: chain G residue   87 THR
Chi-restraints excluded: chain G residue   89 THR
Chi-restraints excluded: chain G residue  125 PHE
Chi-restraints excluded: chain G residue  154 LEU
Chi-restraints excluded: chain G residue  161 MET
Chi-restraints excluded: chain G residue  181 ILE
Chi-restraints excluded: chain G residue  206 THR
Chi-restraints excluded: chain G residue  221 LEU
Chi-restraints excluded: chain H residue   46 LEU
Chi-restraints excluded: chain H residue   55 GLU
Chi-restraints excluded: chain H residue   95 THR
Chi-restraints excluded: chain H residue  111 ILE
Chi-restraints excluded: chain H residue  122 ASP
Chi-restraints excluded: chain H residue  182 ILE
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain H residue  245 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 215 optimal weight:    1.9990
   chunk 133 optimal weight:    0.9990
   chunk 128 optimal weight:    0.8980
   chunk 175 optimal weight:    0.9990
   chunk 213 optimal weight:   20.0000
   chunk 238 optimal weight:   10.0000
   chunk 98 optimal weight:    2.9990
   chunk 163 optimal weight:    1.9990
   chunk 116 optimal weight:    6.9990
   chunk 127 optimal weight:    7.9990
   chunk 250 optimal weight:    3.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 406 ASN
** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 608 GLN
B 220 ASN
** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 190 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.183573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.127855 restraints weight = 28410.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 3.49
r_work: 0.3299 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.5228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  20723  Z= 0.170
  Angle     :  0.599   9.374  28038  Z= 0.298
  Chirality :  0.042   0.268   3291
  Planarity :  0.004   0.035   3551
  Dihedral  :  7.416 115.159   2818
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 22.10 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.17), residues: 2527
  helix:  1.57 (0.15), residues: 1155
  sheet: -0.10 (0.24), residues: 475
  loop : -0.80 (0.20), residues: 897

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 266 
 HIS   0.004   0.001   HIS A 506 
 PHE   0.021   0.002   PHE A 509 
 TYR   0.025   0.002   TYR E 161 
 ARG   0.007   0.000   ARG E  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03842 ( 1047)
  hydrogen bonds       : angle       4.46872 ( 3015)
  covalent geometry    : bond        0.00407 (20723)
  covalent geometry    : angle       0.59898 (28038)

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

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

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  381 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 290
  time to evaluate  : 4.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ARG cc_start: 0.8087 (mmt-90) cc_final: 0.7799 (mmt-90)
REVERT: A  351 MET cc_start: 0.9309 (mmt) cc_final: 0.8952 (mmt)
REVERT: A  462 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6954 (mttt)
REVERT: A  505 MET cc_start: 0.8799 (tpp) cc_final: 0.8343 (mmt)
REVERT: A  528 LEU cc_start: 0.6354 (OUTLIER) cc_final: 0.5864 (tp)
REVERT: A  588 MET cc_start: 0.7751 (mmp) cc_final: 0.7118 (mtm)
REVERT: C  109 LYS cc_start: 0.6807 (OUTLIER) cc_final: 0.6077 (mptt)
REVERT: C  316 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7592 (t0)
REVERT: D   61 MET cc_start: 0.7647 (pmm) cc_final: 0.7002 (ptp)
REVERT: D   81 GLU cc_start: 0.7549 (tt0) cc_final: 0.6959 (mt-10)
REVERT: D  131 CYS cc_start: 0.8607 (p) cc_final: 0.7661 (t)
REVERT: D  188 ARG cc_start: 0.7190 (ttt-90) cc_final: 0.6929 (ttt-90)
REVERT: E  101 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7180 (ptt)
REVERT: E  224 GLN cc_start: 0.8737 (tt0) cc_final: 0.8346 (mt0)
REVERT: F  126 LEU cc_start: 0.3144 (mt) cc_final: 0.2761 (tp)
REVERT: F  196 LYS cc_start: 0.4316 (mmtt) cc_final: 0.3884 (tptp)
REVERT: F  249 PHE cc_start: 0.5355 (m-80) cc_final: 0.3733 (m-80)
REVERT: G   19 PHE cc_start: 0.6930 (t80) cc_final: 0.6477 (t80)
REVERT: G   67 THR cc_start: 0.7421 (OUTLIER) cc_final: 0.6923 (p)
REVERT: G  125 PHE cc_start: 0.6360 (OUTLIER) cc_final: 0.6020 (t80)
REVERT: G  165 GLU cc_start: 0.5862 (tp30) cc_final: 0.5442 (tm-30)
REVERT: H    7 GLU cc_start: 0.7872 (mp0) cc_final: 0.6964 (pm20)
REVERT: H   24 GLN cc_start: 0.8211 (tt0) cc_final: 0.7837 (mt0)
REVERT: H   58 GLN cc_start: 0.8282 (tt0) cc_final: 0.7614 (mt0)
REVERT: H   80 ARG cc_start: 0.8026 (ttp-110) cc_final: 0.7649 (mtm110)
REVERT: H  122 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.7028 (p0)
REVERT: H  124 ASP cc_start: 0.6983 (t70) cc_final: 0.5547 (p0)
REVERT: H  224 ARG cc_start: 0.6812 (mtp85) cc_final: 0.6523 (mtp85)
REVERT: H  245 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7364 (p90)
  outliers start: 91
  outliers final: 71
  residues processed: 363
  average time/residue: 0.4472
  time to fit residues: 259.6047
Evaluate side-chains
  351 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 271
  time to evaluate  : 4.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  372 ARG
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  558 ASN
Chi-restraints excluded: chain A residue  596 ILE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  109 LYS
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  311 SER
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  164 THR
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain E residue   12 SER
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   89 SER
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  101 MET
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain E residue  109 ILE
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  206 VAL
Chi-restraints excluded: chain E residue  246 LEU
Chi-restraints excluded: chain E residue  251 SER
Chi-restraints excluded: chain E residue  353 LEU
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   21 ASP
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue  188 MET
Chi-restraints excluded: chain G residue    2 LEU
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   63 ASP
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   73 THR
Chi-restraints excluded: chain G residue   87 THR
Chi-restraints excluded: chain G residue  125 PHE
Chi-restraints excluded: chain G residue  154 LEU
Chi-restraints excluded: chain G residue  161 MET
Chi-restraints excluded: chain G residue  181 ILE
Chi-restraints excluded: chain G residue  221 LEU
Chi-restraints excluded: chain H residue   46 LEU
Chi-restraints excluded: chain H residue   67 THR
Chi-restraints excluded: chain H residue   95 THR
Chi-restraints excluded: chain H residue  111 ILE
Chi-restraints excluded: chain H residue  122 ASP
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  182 ILE
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain H residue  245 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 2 optimal weight:    0.0470
   chunk 137 optimal weight:    2.9990
   chunk 135 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 244 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 224 optimal weight:    1.9990
   chunk 147 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    1.1282

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

Flipped N/Q/H residues before XYZ refinement:
A 406 ASN
** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 317 HIS
** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 190 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.184371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.125369 restraints weight = 28148.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 2.87
r_work: 0.3302 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.5340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  20723  Z= 0.151
  Angle     :  0.587   9.197  28038  Z= 0.292
  Chirality :  0.042   0.284   3291
  Planarity :  0.004   0.039   3551
  Dihedral  :  7.365 114.885   2818
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 22.15 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.17), residues: 2527
  helix:  1.65 (0.15), residues: 1155
  sheet: -0.09 (0.24), residues: 475
  loop : -0.78 (0.20), residues: 897

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 266 
 HIS   0.003   0.001   HIS A 506 
 PHE   0.022   0.001   PHE A 722 
 TYR   0.024   0.001   TYR E 161 
 ARG   0.008   0.000   ARG D 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03693 ( 1047)
  hydrogen bonds       : angle       4.41365 ( 3015)
  covalent geometry    : bond        0.00358 (20723)
  covalent geometry    : angle       0.58676 (28038)

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

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

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 278
  time to evaluate  : 2.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ARG cc_start: 0.8110 (mmt-90) cc_final: 0.7897 (mmt-90)
REVERT: A  462 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.6992 (mttt)
REVERT: A  505 MET cc_start: 0.8763 (tpp) cc_final: 0.8302 (mmt)
REVERT: A  528 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6008 (tp)
REVERT: A  588 MET cc_start: 0.7689 (mmp) cc_final: 0.7100 (mtm)
REVERT: B  321 ASN cc_start: 0.7537 (m-40) cc_final: 0.7300 (m110)
REVERT: C  109 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6052 (mptt)
REVERT: C  316 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7542 (t0)
REVERT: D   81 GLU cc_start: 0.7576 (tt0) cc_final: 0.7013 (mt-10)
REVERT: D  131 CYS cc_start: 0.8538 (p) cc_final: 0.7636 (t)
REVERT: D  132 PRO cc_start: 0.8067 (Cg_exo) cc_final: 0.7774 (Cg_endo)
REVERT: D  188 ARG cc_start: 0.7182 (ttt-90) cc_final: 0.6936 (ttt-90)
REVERT: E  101 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7171 (ptt)
REVERT: E  224 GLN cc_start: 0.8746 (tt0) cc_final: 0.8385 (mt0)
REVERT: F  126 LEU cc_start: 0.3232 (mt) cc_final: 0.2847 (tp)
REVERT: F  196 LYS cc_start: 0.4281 (mmtt) cc_final: 0.3835 (tptp)
REVERT: F  249 PHE cc_start: 0.5317 (m-80) cc_final: 0.3669 (m-80)
REVERT: G   67 THR cc_start: 0.7432 (OUTLIER) cc_final: 0.6920 (p)
REVERT: G  149 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.7565 (mtm-85)
REVERT: G  165 GLU cc_start: 0.5744 (tp30) cc_final: 0.5357 (tm-30)
REVERT: H    7 GLU cc_start: 0.7795 (mp0) cc_final: 0.6935 (pm20)
REVERT: H   24 GLN cc_start: 0.8237 (tt0) cc_final: 0.7904 (mt0)
REVERT: H   55 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6709 (mp0)
REVERT: H   58 GLN cc_start: 0.8222 (tt0) cc_final: 0.7586 (mt0)
REVERT: H   80 ARG cc_start: 0.7925 (ttp-110) cc_final: 0.7585 (mtm110)
REVERT: H  122 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6999 (p0)
REVERT: H  124 ASP cc_start: 0.6978 (t70) cc_final: 0.5468 (p0)
REVERT: H  224 ARG cc_start: 0.6888 (mtp85) cc_final: 0.6659 (mtp85)
  outliers start: 90
  outliers final: 69
  residues processed: 345
  average time/residue: 0.3232
  time to fit residues: 173.8839
Evaluate side-chains
  352 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 275
  time to evaluate  : 2.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  372 ARG
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  596 ILE
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  109 LYS
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  311 SER
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  164 THR
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  266 ASP
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain E residue   12 SER
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  101 MET
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain E residue  109 ILE
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  206 VAL
Chi-restraints excluded: chain E residue  246 LEU
Chi-restraints excluded: chain E residue  251 SER
Chi-restraints excluded: chain E residue  353 LEU
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   21 ASP
Chi-restraints excluded: chain F residue   28 PHE
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue  188 MET
Chi-restraints excluded: chain G residue    1 MET
Chi-restraints excluded: chain G residue    2 LEU
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   73 THR
Chi-restraints excluded: chain G residue   87 THR
Chi-restraints excluded: chain G residue  154 LEU
Chi-restraints excluded: chain G residue  161 MET
Chi-restraints excluded: chain G residue  181 ILE
Chi-restraints excluded: chain G residue  221 LEU
Chi-restraints excluded: chain H residue   46 LEU
Chi-restraints excluded: chain H residue   55 GLU
Chi-restraints excluded: chain H residue   95 THR
Chi-restraints excluded: chain H residue  111 ILE
Chi-restraints excluded: chain H residue  122 ASP
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  182 ILE
Chi-restraints excluded: chain H residue  203 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 221 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 228 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 69 optimal weight:    0.2980
   chunk 99 optimal weight:    7.9990
   chunk 116 optimal weight:    2.9990
   chunk 245 optimal weight:    5.9990
   chunk 205 optimal weight:    0.7980
   chunk 145 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 362 GLN
A 406 ASN
** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 321 ASN
** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 190 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.184159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.134183 restraints weight = 28310.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.89
r_work: 0.3306 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.5433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  20723  Z= 0.156
  Angle     :  0.591   9.194  28038  Z= 0.293
  Chirality :  0.042   0.279   3291
  Planarity :  0.004   0.050   3551
  Dihedral  :  7.346 114.623   2818
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.32 %
    Favored  : 73.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.17), residues: 2527
  helix:  1.67 (0.15), residues: 1155
  sheet: -0.11 (0.24), residues: 476
  loop : -0.77 (0.20), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 266 
 HIS   0.004   0.001   HIS B 317 
 PHE   0.020   0.001   PHE A 722 
 TYR   0.020   0.001   TYR E 161 
 ARG   0.009   0.000   ARG D 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03680 ( 1047)
  hydrogen bonds       : angle       4.40840 ( 3015)
  covalent geometry    : bond        0.00373 (20723)
  covalent geometry    : angle       0.59098 (28038)

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

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

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5054 Ramachandran restraints generated.
    2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  365 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 278
  time to evaluate  : 2.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 MET cc_start: 0.9199 (mmt) cc_final: 0.8807 (mmt)
REVERT: A  462 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7038 (mttt)
REVERT: A  486 ASP cc_start: 0.7696 (m-30) cc_final: 0.7407 (t0)
REVERT: A  505 MET cc_start: 0.8702 (tpp) cc_final: 0.8229 (mmt)
REVERT: A  528 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6139 (tp)
REVERT: A  588 MET cc_start: 0.7667 (mmp) cc_final: 0.7133 (mtm)
REVERT: C  109 LYS cc_start: 0.6638 (OUTLIER) cc_final: 0.6041 (mptt)
REVERT: C  316 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7554 (t0)
REVERT: D   61 MET cc_start: 0.7537 (pmm) cc_final: 0.6888 (ptp)
REVERT: D   81 GLU cc_start: 0.7552 (tt0) cc_final: 0.6992 (mt-10)
REVERT: D  131 CYS cc_start: 0.8479 (p) cc_final: 0.7668 (t)
REVERT: D  157 MET cc_start: 0.6820 (ptt) cc_final: 0.6115 (tpp)
REVERT: D  188 ARG cc_start: 0.7172 (ttt-90) cc_final: 0.6918 (ttt-90)
REVERT: E  224 GLN cc_start: 0.8745 (tt0) cc_final: 0.8421 (mt0)
REVERT: F  126 LEU cc_start: 0.3255 (mt) cc_final: 0.2887 (tp)
REVERT: F  196 LYS cc_start: 0.4271 (mmtt) cc_final: 0.3817 (tptp)
REVERT: F  249 PHE cc_start: 0.5321 (m-80) cc_final: 0.3641 (m-80)
REVERT: G   19 PHE cc_start: 0.7149 (t80) cc_final: 0.6879 (t80)
REVERT: G   48 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7790 (p)
REVERT: G  149 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.7640 (mtm-85)
REVERT: G  165 GLU cc_start: 0.5716 (tp30) cc_final: 0.5402 (tm-30)
REVERT: G  224 ARG cc_start: 0.6599 (OUTLIER) cc_final: 0.5778 (tmm-80)
REVERT: H    7 GLU cc_start: 0.7731 (mp0) cc_final: 0.6905 (pm20)
REVERT: H   24 GLN cc_start: 0.8249 (tt0) cc_final: 0.7814 (mt0)
REVERT: H   55 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6720 (mp0)
REVERT: H   58 GLN cc_start: 0.8209 (tt0) cc_final: 0.7598 (mt0)
REVERT: H   80 ARG cc_start: 0.7905 (ttp-110) cc_final: 0.7571 (mtm110)
REVERT: H  122 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.7028 (p0)
REVERT: H  124 ASP cc_start: 0.7024 (t70) cc_final: 0.5534 (p0)
  outliers start: 87
  outliers final: 73
  residues processed: 343
  average time/residue: 0.3356
  time to fit residues: 179.1781
Evaluate side-chains
  353 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 272
  time to evaluate  : 2.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  372 ARG
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  596 ILE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  109 LYS
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  311 SER
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  164 THR
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  266 ASP
Chi-restraints excluded: chain D residue  330 ASP
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain E residue   12 SER
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  101 MET
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain E residue  109 ILE
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  206 VAL
Chi-restraints excluded: chain E residue  246 LEU
Chi-restraints excluded: chain E residue  251 SER
Chi-restraints excluded: chain E residue  353 LEU
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   21 ASP
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue  181 ILE
Chi-restraints excluded: chain F residue  188 MET
Chi-restraints excluded: chain G residue    1 MET
Chi-restraints excluded: chain G residue    2 LEU
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   73 THR
Chi-restraints excluded: chain G residue   87 THR
Chi-restraints excluded: chain G residue  154 LEU
Chi-restraints excluded: chain G residue  161 MET
Chi-restraints excluded: chain G residue  181 ILE
Chi-restraints excluded: chain G residue  221 LEU
Chi-restraints excluded: chain G residue  224 ARG
Chi-restraints excluded: chain H residue   46 LEU
Chi-restraints excluded: chain H residue   55 GLU
Chi-restraints excluded: chain H residue   95 THR
Chi-restraints excluded: chain H residue  111 ILE
Chi-restraints excluded: chain H residue  122 ASP
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  182 ILE
Chi-restraints excluded: chain H residue  203 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 251
   random chunks:
   chunk 133 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 165 optimal weight:    7.9990
   chunk 248 optimal weight:    0.8980
   chunk 166 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 223 optimal weight:    9.9990
   chunk 245 optimal weight:    0.0770
   chunk 92 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.7540

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

Flipped N/Q/H residues before XYZ refinement:
A 362 GLN
A 406 ASN
** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 GLN
** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 144 ASN
G 190 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.185729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.126666 restraints weight = 28295.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 2.97
r_work: 0.3320 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.5501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  20723  Z= 0.123
  Angle     :  0.572   9.155  28038  Z= 0.283
  Chirality :  0.041   0.305   3291
  Planarity :  0.004   0.042   3551
  Dihedral  :  7.260 113.847   2818
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 22.67 %
    Favored  : 73.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.17), residues: 2527
  helix:  1.77 (0.15), residues: 1156
  sheet: -0.04 (0.24), residues: 475
  loop : -0.74 (0.20), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 266 
 HIS   0.003   0.001   HIS B 317 
 PHE   0.020   0.001   PHE A 509 
 TYR   0.020   0.001   TYR D  83 
 ARG   0.010   0.000   ARG D 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03434 ( 1047)
  hydrogen bonds       : angle       4.34497 ( 3015)
  covalent geometry    : bond        0.00288 (20723)
  covalent geometry    : angle       0.57205 (28038)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11671.28 seconds
wall clock time: 202 minutes 15.78 seconds (12135.78 seconds total)