Starting phenix.real_space_refine
on Thu Mar 13 22:06:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yiy_33866/03_2025/7yiy_33866.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yiy_33866/03_2025/7yiy_33866.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yiy_33866/03_2025/7yiy_33866.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yiy_33866/03_2025/7yiy_33866.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yiy_33866/03_2025/7yiy_33866.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yiy_33866/03_2025/7yiy_33866.cif"
  }
  resolution = 2.7
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      52      5.16       5
     C    5971      2.51       5
     N    1559      2.21       5
     O    1674      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 82 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9257
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 3940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 499, 3940
          Classifications: {'peptide': 499}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 17, 'TRANS': 481}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "E"
      Number of atoms: 324
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 324
          Classifications: {'peptide': 41}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 39}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "D"
      Number of atoms: 1236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 153, 1236
          Classifications: {'peptide': 153}
          Link IDs: {'PTRANS': 8, 'TRANS': 144}
    Chain: "C"
      Number of atoms: 411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 411
          Classifications: {'peptide': 48}
          Link IDs: {'PTRANS': 1, 'TRANS': 46}
    Chain: "A"
      Number of atoms: 3285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 3285
          Classifications: {'peptide': 423}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 21, 'TRANS': 401}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'PLP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 46
          Unusual residues: {'Z1T': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.92, per 1000 atoms: 0.64
  Number of scatterers: 9257
  At special positions: 0
  Unit cell: (91.8, 85.32, 122.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     P       1     15.00
     O    1674      8.00
     N    1559      7.00
     C    5971      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.35
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2156

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 11 sheets defined
      53.9% alpha, 9.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'B' and resid 67 through 92
      removed outlier: 3.855A  pdb=" N   TYR B  75 " --> pdb=" O   ALA B  71 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL B  76 " --> pdb=" O   VAL B  72 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLY B  77 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 109
      removed outlier: 3.530A  pdb=" N   GLN B 108 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LYS B 109 " --> pdb=" O   GLU B 106 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 105 through 109'
    Processing helix  chain 'B' and resid 120 through 126
    Processing helix  chain 'B' and resid 127 through 134
      removed outlier: 3.942A  pdb=" N   ARG B 131 " --> pdb=" O   MET B 128 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   ASP B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   TRP B 134 " --> pdb=" O   ARG B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 181
      removed outlier: 4.281A  pdb=" N   PHE B 181 " --> pdb=" O   TYR B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 199
      removed outlier: 3.513A  pdb=" N   GLU B 190 " --> pdb=" O   GLY B 186 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLU B 198 " --> pdb=" O   LYS B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 228
      removed outlier: 3.614A  pdb=" N   GLU B 217 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA B 224 " --> pdb=" O   GLU B 220 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ARG B 225 " --> pdb=" O   GLU B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 244
      removed outlier: 3.781A  pdb=" N   ASN B 242 " --> pdb=" O   GLY B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 249
    Processing helix  chain 'B' and resid 263 through 274
      removed outlier: 4.033A  pdb=" N   GLY B 274 " --> pdb=" O   ALA B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 299
      removed outlier: 3.692A  pdb=" N   ILE B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL B 297 " --> pdb=" O   LYS B 293 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   TYR B 298 " --> pdb=" O   ASP B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 337
      removed outlier: 3.803A  pdb=" N   LYS B 336 " --> pdb=" O   ALA B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 363
      removed outlier: 4.133A  pdb=" N   GLU B 361 " --> pdb=" O   ARG B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 370
    Processing helix  chain 'B' and resid 391 through 402
      removed outlier: 3.749A  pdb=" N   THR B 400 " --> pdb=" O   ASP B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 408
      removed outlier: 3.507A  pdb=" N   VAL B 406 " --> pdb=" O   SER B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 428
      removed outlier: 3.522A  pdb=" N   GLN B 418 " --> pdb=" O   PRO B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 455
      removed outlier: 3.713A  pdb=" N   GLU B 437 " --> pdb=" O   SER B 433 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   CYS B 438 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL B 439 " --> pdb=" O   GLY B 435 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ALA B 443 " --> pdb=" O   VAL B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 489
      removed outlier: 3.942A  pdb=" N   GLY B 480 " --> pdb=" O   PRO B 476 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLY B 483 " --> pdb=" O   ILE B 479 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ARG B 484 " --> pdb=" O   GLY B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 536
    Processing helix  chain 'E' and resid 10 through 19
    Processing helix  chain 'E' and resid 21 through 40
      removed outlier: 3.527A  pdb=" N   LEU E  25 " --> pdb=" O   PRO E  21 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LEU E  27 " --> pdb=" O   TYR E  23 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLU E  28 " --> pdb=" O   HIS E  24 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ARG E  37 " --> pdb=" O   LEU E  33 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 11 through 19
      removed outlier: 3.766A  pdb=" N   ARG D  15 " --> pdb=" O   PRO D  12 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL D  16 " --> pdb=" O   ASN D  13 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   MET D  17 " --> pdb=" O   THR D  14 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 21 through 39
      removed outlier: 3.599A  pdb=" N   ILE D  30 " --> pdb=" O   TYR D  26 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 66
    Processing helix  chain 'D' and resid 84 through 89
    Processing helix  chain 'D' and resid 90 through 93
    Processing helix  chain 'D' and resid 96 through 116
      Proline residue:  D 106  - end of helix
    Processing helix  chain 'D' and resid 120 through 133
      removed outlier: 3.789A  pdb=" N   VAL D 125 " --> pdb=" O   GLN D 121 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU D 126 " --> pdb=" O   ILE D 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 134 through 143
      Proline residue:  D 137  - end of helix
      Proline residue:  D 140  - end of helix
      removed outlier: 3.531A  pdb=" N   HIS D 143 " --> pdb=" O   PRO D 140 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 134 through 143'
    Processing helix  chain 'D' and resid 146 through 150
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 25 through 29
      removed outlier: 3.614A  pdb=" N   MET C  28 " --> pdb=" O   ALA C  25 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 55
      removed outlier: 3.614A  pdb=" N   VAL C  36 " --> pdb=" O   TRP C  32 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE C  37 " --> pdb=" O   GLU C  33 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   ILE C  44 " --> pdb=" O   MET C  40 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR C  51 " --> pdb=" O   MET C  47 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TYR C  53 " --> pdb=" O   LEU C  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 64
      removed outlier: 3.527A  pdb=" N   LYS A  57 " --> pdb=" O   THR A  53 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLU A  58 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLU A  59 " --> pdb=" O   LYS A  55 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   TRP A  64 " --> pdb=" O   LEU A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 129
      removed outlier: 3.676A  pdb=" N   LYS A 127 " --> pdb=" O   ALA A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 157
    Processing helix  chain 'A' and resid 168 through 179
      removed outlier: 3.756A  pdb=" N   ALA A 172 " --> pdb=" O   PHE A 168 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
    Processing helix  chain 'A' and resid 192 through 202
    Processing helix  chain 'A' and resid 213 through 230
      removed outlier: 3.789A  pdb=" N   LEU A 217 " --> pdb=" O   ASP A 213 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ILE A 226 " --> pdb=" O   LYS A 222 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLU A 227 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS A 230 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 236
    Processing helix  chain 'A' and resid 257 through 268
      removed outlier: 3.641A  pdb=" N   LYS A 262 " --> pdb=" O   PRO A 258 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU A 263 " --> pdb=" O   GLU A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 294
    Processing helix  chain 'A' and resid 296 through 300
      removed outlier: 3.545A  pdb=" N   ILE A 300 " --> pdb=" O   ILE A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 326
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 342 through 359
      removed outlier: 3.537A  pdb=" N   GLU A 351 " --> pdb=" O   ALA A 347 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ASN A 359 " --> pdb=" O   ILE A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 377
      removed outlier: 3.942A  pdb=" N   GLN A 372 " --> pdb=" O   GLU A 368 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ILE A 373 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   HIS A 374 " --> pdb=" O   CYS A 370 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   LYS A 375 " --> pdb=" O   GLY A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 420
      removed outlier: 3.695A  pdb=" N   ASP A 408 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE A 415 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 436
      removed outlier: 4.138A  pdb=" N   GLU A 436 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 469
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 48
    Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 62
    Processing sheet with id=AA3, first strand: chain 'B' and resid 137 through 138
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 152
      removed outlier: 5.156A  pdb=" N   ILE B 148 " --> pdb=" O   LYS B 168 " (cutoff:3.500A)
      removed outlier: 5.511A  pdb=" N   LYS B 168 " --> pdb=" O   ILE B 148 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   GLU B 150 " --> pdb=" O   ILE B 166 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ILE B 166 " --> pdb=" O   GLU B 150 " (cutoff:3.500A)
      removed outlier: 11.136A  pdb=" N   GLN B 152 " --> pdb=" O   GLY B 164 " (cutoff:3.500A)
      removed outlier: 9.614A  pdb=" N   GLY B 164 " --> pdb=" O   GLN B 152 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   GLY B 492 " --> pdb=" O   GLY B 169 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ILE B 171 " --> pdb=" O   GLY B 492 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 234
      removed outlier: 8.201A  pdb=" N   GLU B 315 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 317 through 318
      removed outlier: 3.575A  pdb=" N   SER B 323 " --> pdb=" O   TYR B 318 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 468 through 472
      removed outlier: 3.833A  pdb=" N   VAL B 494 " --> pdb=" O   ARG B 509 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 94
      removed outlier: 7.433A  pdb=" N   ALA A 425 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 160 through 164
      removed outlier: 8.558A  pdb=" N   SER A 304 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   LEU A 273 " --> pdb=" O   SER A 304 " (cutoff:3.500A)
      removed outlier: 9.095A  pdb=" N   ASN A 306 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ARG A 240 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   PHE A 272 " --> pdb=" O   ARG A 240 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   ILE A 242 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   GLU A 274 " --> pdb=" O   ILE A 242 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL A 244 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   GLU A 245 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 383 through 386
    Processing sheet with id=AB2, first strand: chain 'A' and resid 427 through 428
      removed outlier: 4.507A  pdb=" N   THR A 427 " --> pdb=" O   ARG A 445 " (cutoff:3.500A)

    419 hydrogen bonds defined for protein.
    1173 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.76

  Time building geometry restraints manager: 2.89 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2604
        1.33 -     1.45: 1510
        1.45 -     1.57: 5255
        1.57 -     1.69: 1
        1.69 -     1.81: 87
  Bond restraints: 9457
  Sorted by residual:
  bond pdb=" C14 Z1T D 201 "
       pdb=" C15 Z1T D 201 "
    ideal  model  delta    sigma   weight residual
    1.329  1.523 -0.194 2.00e-02 2.50e+03 9.45e+01
  bond pdb=" C2  PLP B 601 "
       pdb=" C3  PLP B 601 "
    ideal  model  delta    sigma   weight residual
    1.390  1.485 -0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" C4  PLP B 601 "
       pdb=" C5  PLP B 601 "
    ideal  model  delta    sigma   weight residual
    1.390  1.483 -0.093 2.00e-02 2.50e+03 2.14e+01
  bond pdb=" C3  PLP B 601 "
       pdb=" C4  PLP B 601 "
    ideal  model  delta    sigma   weight residual
    1.390  1.480 -0.090 2.00e-02 2.50e+03 2.04e+01
  bond pdb=" C   PHE B 498 "
       pdb=" O   PHE B 498 "
    ideal  model  delta    sigma   weight residual
    1.241  1.212  0.029 9.80e-03 1.04e+04 8.78e+00
  ... (remaining 9452 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 12423
        2.43 -     4.85: 301
        4.85 -     7.28: 50
        7.28 -     9.70: 8
        9.70 -    12.13: 5
  Bond angle restraints: 12787
  Sorted by residual:
  angle pdb=" N   ILE B 503 "
        pdb=" CA  ILE B 503 "
        pdb=" C   ILE B 503 "
      ideal   model   delta    sigma   weight residual
     110.62  118.43   -7.81 1.02e+00 9.61e-01 5.86e+01
  angle pdb=" N   GLN B 116 "
        pdb=" CA  GLN B 116 "
        pdb=" C   GLN B 116 "
      ideal   model   delta    sigma   weight residual
     109.76   99.56   10.20 1.59e+00 3.96e-01 4.12e+01
  angle pdb=" N   PRO A  78 "
        pdb=" CA  PRO A  78 "
        pdb=" CB  PRO A  78 "
      ideal   model   delta    sigma   weight residual
     103.44  109.98   -6.54 1.12e+00 7.97e-01 3.41e+01
  angle pdb=" N   GLY B 497 "
        pdb=" CA  GLY B 497 "
        pdb=" C   GLY B 497 "
      ideal   model   delta    sigma   weight residual
     112.81  120.13   -7.32 1.38e+00 5.25e-01 2.82e+01
  angle pdb=" N   ASN B  60 "
        pdb=" CA  ASN B  60 "
        pdb=" C   ASN B  60 "
      ideal   model   delta    sigma   weight residual
     108.34  116.90   -8.56 1.64e+00 3.72e-01 2.72e+01
  ... (remaining 12782 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.31: 4933
       16.31 -    32.63: 482
       32.63 -    48.94: 174
       48.94 -    65.26: 66
       65.26 -    81.57: 12
  Dihedral angle restraints: 5667
    sinusoidal: 2298
      harmonic: 3369
  Sorted by residual:
  dihedral pdb=" CA  ASN B 120 "
           pdb=" C   ASN B 120 "
           pdb=" N   PHE B 121 "
           pdb=" CA  PHE B 121 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.33   24.67     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" CA  ILE B  96 "
           pdb=" C   ILE B  96 "
           pdb=" N   GLU B  97 "
           pdb=" CA  GLU B  97 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.19  -21.81     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" C   TYR E  44 "
           pdb=" N   TYR E  44 "
           pdb=" CA  TYR E  44 "
           pdb=" CB  TYR E  44 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.97   10.37     0      2.50e+00 1.60e-01 1.72e+01
  ... (remaining 5664 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 1247
       0.087 -    0.174: 157
       0.174 -    0.261: 19
       0.261 -    0.347: 2
       0.347 -    0.434: 3
  Chirality restraints: 1428
  Sorted by residual:
  chirality pdb=" CA  LYS B 168 "
            pdb=" N   LYS B 168 "
            pdb=" C   LYS B 168 "
            pdb=" CB  LYS B 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.71e+00
  chirality pdb=" CA  TYR E  44 "
            pdb=" N   TYR E  44 "
            pdb=" C   TYR E  44 "
            pdb=" CB  TYR E  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.59e+00
  chirality pdb=" CA  PHE B 498 "
            pdb=" N   PHE B 498 "
            pdb=" C   PHE B 498 "
            pdb=" CB  PHE B 498 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.41 2.00e-01 2.50e+01 4.10e+00
  ... (remaining 1425 not shown)

  Planarity restraints: 1619
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 501 "   -0.057 5.00e-02 4.00e+02   8.65e-02 1.20e+01
        pdb=" N   PRO B 502 "    0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO B 502 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO B 502 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 166 "    0.022 2.00e-02 2.50e+03   1.68e-02 5.62e+00
        pdb=" CG  TYR A 166 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 166 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 166 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 166 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 166 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 166 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 166 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 501 "   -0.011 2.00e-02 2.50e+03   2.23e-02 4.98e+00
        pdb=" C   THR B 501 "    0.039 2.00e-02 2.50e+03
        pdb=" O   THR B 501 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   PRO B 502 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1616 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 1023
        2.74 -     3.28: 8357
        3.28 -     3.82: 14320
        3.82 -     4.36: 18141
        4.36 -     4.90: 31287
  Nonbonded interactions: 73128
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 201 "
            pdb=" OG  SER B 412 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OH  TYR B 407 "
            pdb=" OE2 GLU A 436 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   THR B  66 "
            pdb=" NH1 ARG D  20 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" OG1 THR B 432 "
            pdb=" CD2 LEU B 434 "
     model   vdw
     2.261 3.460
  nonbonded pdb=" NZ  LYS B 338 "
            pdb=" O   TRP A  64 "
     model   vdw
     2.296 3.120
  ... (remaining 73123 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.80 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     25.650
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:15.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
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      :  0.008   0.194   9457  Z= 0.503
  Angle     :  0.981  12.129  12787  Z= 0.587
  Chirality :  0.063   0.434   1428
  Planarity :  0.006   0.086   1619
  Dihedral  : 16.225  81.572   3511
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  5.20 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  :  2.44 %
    Favored  : 92.79 %
  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: -1.48 (0.24), residues: 1154
  helix: -0.40 (0.22), residues: 505
  sheet: -0.01 (0.50), residues: 118
  loop : -1.77 (0.25), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 134 
 HIS   0.005   0.001   HIS A  91 
 PHE   0.032   0.003   PHE A 138 
 TYR   0.039   0.003   TYR A 166 
 ARG   0.007   0.001   ARG D  81 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 125
  time to evaluate  : 1.031 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6711 (m-10)
REVERT: B  152 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8163 (pm20)
REVERT: B  183 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.8112 (ptm160)
REVERT: B  281 LYS cc_start: 0.8394 (mttp) cc_final: 0.8153 (mttt)
REVERT: B  344 ASP cc_start: 0.8647 (t0) cc_final: 0.8445 (t70)
REVERT: B  427 MET cc_start: 0.9006 (mtm) cc_final: 0.8589 (mtm)
REVERT: B  434 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6958 (tp)
REVERT: B  436 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7592 (mtpp)
REVERT: B  518 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8162 (tppt)
REVERT: E   42 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6616 (mmtm)
REVERT: C   11 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7289 (tmtt)
REVERT: C   13 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7928 (mmp)
REVERT: A   56 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7444 (mp0)
REVERT: A  375 LYS cc_start: 0.8657 (tttm) cc_final: 0.8448 (tttp)
REVERT: A  434 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8239 (mmpt)
REVERT: A  435 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6522 (mp0)
REVERT: A  459 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7018 (tmm-80)
  outliers start: 47
  outliers final: 22
  residues processed: 149
  average time/residue: 1.8217
  time to fit residues: 284.9202
Evaluate side-chains
  145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 110
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  109 LYS
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  152 GLN
Chi-restraints excluded: chain B residue  168 LYS
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  190 GLU
Chi-restraints excluded: chain B residue  194 LYS
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  436 LYS
Chi-restraints excluded: chain B residue  496 VAL
Chi-restraints excluded: chain B residue  518 LYS
Chi-restraints excluded: chain B residue  526 LYS
Chi-restraints excluded: chain B residue  530 GLU
Chi-restraints excluded: chain B residue  541 ARG
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue   44 TYR
Chi-restraints excluded: chain E residue   45 LYS
Chi-restraints excluded: chain C residue   11 LYS
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  420 MET
Chi-restraints excluded: chain A residue  422 ARG
Chi-restraints excluded: chain A residue  434 LYS
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  459 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 86 optimal weight:    0.7980
   chunk 47 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 89 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
B 189 GLN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 229 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.115087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.094750 restraints weight = 11305.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 1.63
r_work: 0.2834 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2714 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2695
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2695 r_free = 0.2695    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2695 r_free = 0.2695    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2695
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.1211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9457  Z= 0.245
  Angle     :  0.641   8.088  12787  Z= 0.344
  Chirality :  0.048   0.183   1428
  Planarity :  0.005   0.054   1619
  Dihedral  : 11.363  73.126   1423
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  :  9.64 %
    Favored  : 87.51 %
  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 (0.24), residues: 1154
  helix:  0.59 (0.23), residues: 527
  sheet:  0.24 (0.49), residues: 117
  loop : -1.75 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 134 
 HIS   0.004   0.001   HIS B 516 
 PHE   0.018   0.002   PHE A 138 
 TYR   0.020   0.002   TYR A 166 
 ARG   0.003   0.000   ARG D  20 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 1.344 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.6747 (m-10)
REVERT: B  150 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7893 (tm-30)
REVERT: B  152 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8512 (pm20)
REVERT: B  197 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8143 (tp30)
REVERT: B  427 MET cc_start: 0.8784 (mtm) cc_final: 0.8424 (mtm)
REVERT: B  434 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.6649 (tp)
REVERT: B  518 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7833 (tppt)
REVERT: B  526 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8278 (ttpp)
REVERT: B  530 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7751 (tt0)
REVERT: D   19 SER cc_start: 0.9041 (m) cc_final: 0.8757 (m)
REVERT: C   11 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7176 (mptt)
REVERT: A   56 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7448 (mp0)
REVERT: A  107 ASN cc_start: 0.8707 (p0) cc_final: 0.8453 (p0)
REVERT: A  205 ASP cc_start: 0.8574 (m-30) cc_final: 0.8295 (m-30)
REVERT: A  434 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8240 (mmpt)
REVERT: A  435 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7166 (mm-30)
  outliers start: 28
  outliers final: 9
  residues processed: 137
  average time/residue: 2.2039
  time to fit residues: 316.7324
Evaluate side-chains
  129 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  109 LYS
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  152 GLN
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain B residue  518 LYS
Chi-restraints excluded: chain B residue  519 GLU
Chi-restraints excluded: chain B residue  526 LYS
Chi-restraints excluded: chain B residue  530 GLU
Chi-restraints excluded: chain E residue   44 TYR
Chi-restraints excluded: chain C residue   11 LYS
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  422 ARG
Chi-restraints excluded: chain A residue  435 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 113 optimal weight:    7.9990
   chunk 33 optimal weight:    8.9990
   chunk 37 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 4 optimal weight:    0.1980
   chunk 49 optimal weight:    0.6980
   chunk 70 optimal weight:    0.3980
   chunk 103 optimal weight:    2.9990
   chunk 60 optimal weight:    0.4980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B 440 GLN
B 463 ASN
A 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.119636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.099352 restraints weight = 11514.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 1.66
r_work: 0.2928 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2811 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2823
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2823 r_free = 0.2823    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2823 r_free = 0.2823    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2823
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9457  Z= 0.137
  Angle     :  0.514   8.104  12787  Z= 0.274
  Chirality :  0.043   0.181   1428
  Planarity :  0.004   0.046   1619
  Dihedral  :  9.560  69.079   1369
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.08 %
    Favored  : 85.89 %
  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:  0.05 (0.25), residues: 1154
  helix:  1.33 (0.24), residues: 537
  sheet:  0.29 (0.48), residues: 119
  loop : -1.52 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 134 
 HIS   0.002   0.000   HIS B  47 
 PHE   0.012   0.001   PHE A 209 
 TYR   0.011   0.001   TYR B 235 
 ARG   0.003   0.000   ARG B 271 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 1.105 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6786 (m-10)
REVERT: B  109 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8204 (mmtt)
REVERT: B  150 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8151 (tt0)
REVERT: B  152 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8519 (pm20)
REVERT: B  189 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7045 (mm-40)
REVERT: B  197 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8240 (tp30)
REVERT: B  427 MET cc_start: 0.8701 (mtm) cc_final: 0.8368 (mtm)
REVERT: B  518 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7873 (tppt)
REVERT: B  530 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7535 (tt0)
REVERT: D   19 SER cc_start: 0.8910 (m) cc_final: 0.8578 (m)
REVERT: A  422 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8278 (mmm-85)
REVERT: A  434 LYS cc_start: 0.8752 (mmtm) cc_final: 0.8315 (mmpt)
REVERT: A  435 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7308 (mm-30)
  outliers start: 20
  outliers final: 4
  residues processed: 133
  average time/residue: 1.6564
  time to fit residues: 231.5928
Evaluate side-chains
  120 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  109 LYS
Chi-restraints excluded: chain B residue  152 GLN
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain B residue  496 VAL
Chi-restraints excluded: chain B residue  518 LYS
Chi-restraints excluded: chain B residue  530 GLU
Chi-restraints excluded: chain E residue   44 TYR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  422 ARG
Chi-restraints excluded: chain A residue  435 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 110 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 109 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 112 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    3.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.110519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.089681 restraints weight = 11424.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 1.66
r_work: 0.2757 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2637 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2623
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2623
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060   9457  Z= 0.494
  Angle     :  0.771   9.336  12787  Z= 0.406
  Chirality :  0.055   0.216   1428
  Planarity :  0.006   0.062   1619
  Dihedral  :  9.459  68.338   1349
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 13.30 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.27 (0.25), residues: 1154
  helix:  1.05 (0.23), residues: 525
  sheet:  0.11 (0.48), residues: 129
  loop : -1.63 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 134 
 HIS   0.005   0.001   HIS A 145 
 PHE   0.028   0.002   PHE A 138 
 TYR   0.018   0.003   TYR A 166 
 ARG   0.006   0.001   ARG A 219 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 1.055 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.6609 (m-10)
REVERT: B  150 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8148 (mt-10)
REVERT: B  152 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8507 (pm20)
REVERT: B  197 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8265 (tp30)
REVERT: B  315 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8947 (mt-10)
REVERT: B  427 MET cc_start: 0.8821 (mtm) cc_final: 0.8556 (mtm)
REVERT: B  436 LYS cc_start: 0.8475 (mtmm) cc_final: 0.7628 (mtpt)
REVERT: B  518 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8069 (tppt)
REVERT: B  530 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7703 (tt0)
REVERT: A   62 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7857 (tp30)
REVERT: A  144 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8473 (p)
REVERT: A  434 LYS cc_start: 0.8857 (mmtm) cc_final: 0.8383 (mmpt)
  outliers start: 32
  outliers final: 12
  residues processed: 131
  average time/residue: 2.0212
  time to fit residues: 278.0734
Evaluate side-chains
  131 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  109 LYS
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  152 GLN
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  315 GLU
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain B residue  518 LYS
Chi-restraints excluded: chain B residue  530 GLU
Chi-restraints excluded: chain E residue   44 TYR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  456 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 96 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 70 optimal weight:    0.5980
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
B 262 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.114661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.093884 restraints weight = 11296.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 1.68
r_work: 0.2786 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2665 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9457  Z= 0.261
  Angle     :  0.626   8.016  12787  Z= 0.333
  Chirality :  0.047   0.198   1428
  Planarity :  0.005   0.056   1619
  Dihedral  :  8.799  67.551   1345
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 13.91 %
    Favored  : 82.84 %
  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: -0.08 (0.25), residues: 1154
  helix:  1.32 (0.23), residues: 526
  sheet:  0.18 (0.48), residues: 122
  loop : -1.65 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 134 
 HIS   0.003   0.001   HIS B  47 
 PHE   0.017   0.002   PHE A 209 
 TYR   0.018   0.002   TYR B 235 
 ARG   0.003   0.000   ARG B 271 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 1.005 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6530 (m-10)
REVERT: B  150 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8093 (mt-10)
REVERT: B  152 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8516 (pm20)
REVERT: B  197 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8235 (tp30)
REVERT: B  427 MET cc_start: 0.8762 (mtm) cc_final: 0.8489 (mtm)
REVERT: B  436 LYS cc_start: 0.8431 (mtmm) cc_final: 0.7734 (mtpt)
REVERT: B  518 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7964 (tppt)
REVERT: B  530 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7653 (tt0)
REVERT: E   13 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.5878 (mtt)
REVERT: D   19 SER cc_start: 0.9076 (m) cc_final: 0.8798 (m)
REVERT: A   62 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7795 (tp30)
REVERT: A  107 ASN cc_start: 0.8791 (p0) cc_final: 0.8496 (p0)
REVERT: A  422 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7718 (mtm-85)
REVERT: A  434 LYS cc_start: 0.8853 (mmtm) cc_final: 0.8398 (mmpt)
  outliers start: 32
  outliers final: 18
  residues processed: 131
  average time/residue: 1.7382
  time to fit residues: 239.6793
Evaluate side-chains
  137 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  109 LYS
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  152 GLN
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain B residue  496 VAL
Chi-restraints excluded: chain B residue  518 LYS
Chi-restraints excluded: chain B residue  519 GLU
Chi-restraints excluded: chain B residue  530 GLU
Chi-restraints excluded: chain B residue  542 HIS
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   44 TYR
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  422 ARG
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  456 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 107 optimal weight:    6.9990
   chunk 43 optimal weight:    0.0980
   chunk 0 optimal weight:   10.0000
   chunk 101 optimal weight:    0.5980
   chunk 108 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.116738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.096334 restraints weight = 11349.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 1.63
r_work: 0.2859 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2741 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2755
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2755 r_free = 0.2755    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2755 r_free = 0.2755    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2755
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9457  Z= 0.173
  Angle     :  0.546   7.478  12787  Z= 0.291
  Chirality :  0.044   0.189   1428
  Planarity :  0.005   0.050   1619
  Dihedral  :  8.324  66.779   1345
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 14.21 %
    Favored  : 82.34 %
  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:  0.24 (0.25), residues: 1154
  helix:  1.68 (0.24), residues: 528
  sheet:  0.04 (0.46), residues: 124
  loop : -1.52 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 134 
 HIS   0.002   0.001   HIS A 292 
 PHE   0.015   0.001   PHE A 209 
 TYR   0.013   0.001   TYR B 235 
 ARG   0.005   0.000   ARG B 271 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 121
  time to evaluate  : 1.124 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.6549 (m-10)
REVERT: B  109 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8200 (mmtt)
REVERT: B  150 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8074 (mt-10)
REVERT: B  152 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8566 (pm20)
REVERT: B  189 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.6974 (mm-40)
REVERT: B  190 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8260 (mt-10)
REVERT: B  197 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8206 (tp30)
REVERT: B  427 MET cc_start: 0.8677 (mtm) cc_final: 0.8389 (mtm)
REVERT: B  475 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.7403 (mtp)
REVERT: B  530 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7599 (tt0)
REVERT: E   13 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.5857 (mtt)
REVERT: D   19 SER cc_start: 0.9021 (m) cc_final: 0.8719 (m)
REVERT: A   56 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7017 (mp0)
REVERT: A   62 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7763 (tp30)
REVERT: A  144 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8350 (p)
REVERT: A  423 SER cc_start: 0.8727 (m) cc_final: 0.8158 (p)
REVERT: A  434 LYS cc_start: 0.8878 (mmtm) cc_final: 0.8424 (mmpt)
REVERT: A  435 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7944 (mm-30)
  outliers start: 34
  outliers final: 15
  residues processed: 138
  average time/residue: 1.6095
  time to fit residues: 234.5286
Evaluate side-chains
  142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  109 LYS
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  152 GLN
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  423 MET
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain B residue  475 MET
Chi-restraints excluded: chain B residue  496 VAL
Chi-restraints excluded: chain B residue  519 GLU
Chi-restraints excluded: chain B residue  530 GLU
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   44 TYR
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  420 MET
Chi-restraints excluded: chain A residue  435 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   overall best weight:    1.3784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.115950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.095276 restraints weight = 11362.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 1.68
r_work: 0.2827 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2707 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2684
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2684 r_free = 0.2684    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2684 r_free = 0.2684    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2684
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9457  Z= 0.221
  Angle     :  0.592   7.510  12787  Z= 0.315
  Chirality :  0.046   0.193   1428
  Planarity :  0.005   0.052   1619
  Dihedral  :  8.197  66.169   1341
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 14.31 %
    Favored  : 82.44 %
  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:  0.25 (0.25), residues: 1154
  helix:  1.67 (0.23), residues: 528
  sheet: -0.08 (0.46), residues: 126
  loop : -1.47 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 134 
 HIS   0.003   0.001   HIS B  47 
 PHE   0.016   0.001   PHE A 209 
 TYR   0.016   0.002   TYR B 235 
 ARG   0.006   0.000   ARG B 271 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 1.124 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6490 (m-10)
REVERT: B  109 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8194 (mmtt)
REVERT: B  150 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8103 (mt-10)
REVERT: B  152 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8513 (pm20)
REVERT: B  197 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8219 (tp30)
REVERT: B  427 MET cc_start: 0.8722 (mtm) cc_final: 0.8463 (mtm)
REVERT: B  475 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.7710 (mtp)
REVERT: B  530 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7629 (tt0)
REVERT: E   13 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5847 (mtt)
REVERT: D   19 SER cc_start: 0.9021 (m) cc_final: 0.8729 (m)
REVERT: A   56 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7093 (mp0)
REVERT: A   62 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7836 (tp30)
REVERT: A  144 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8357 (p)
REVERT: A  407 GLN cc_start: 0.7836 (mt0) cc_final: 0.7535 (mt0)
REVERT: A  422 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7535 (mtm-85)
REVERT: A  423 SER cc_start: 0.8730 (m) cc_final: 0.8164 (p)
REVERT: A  434 LYS cc_start: 0.8836 (mmtm) cc_final: 0.8384 (mmpt)
REVERT: A  435 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7989 (mm-30)
  outliers start: 32
  outliers final: 13
  residues processed: 134
  average time/residue: 1.7445
  time to fit residues: 245.8974
Evaluate side-chains
  136 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  109 LYS
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  152 GLN
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain B residue  475 MET
Chi-restraints excluded: chain B residue  488 LYS
Chi-restraints excluded: chain B residue  519 GLU
Chi-restraints excluded: chain B residue  530 GLU
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   44 TYR
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  422 ARG
Chi-restraints excluded: chain A residue  435 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   chunk 74 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9980
   chunk 92 optimal weight:    0.1980
   overall best weight:    1.3984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.115471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.094725 restraints weight = 11461.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 1.69
r_work: 0.2826 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9457  Z= 0.222
  Angle     :  0.591   8.547  12787  Z= 0.315
  Chirality :  0.046   0.193   1428
  Planarity :  0.005   0.052   1619
  Dihedral  :  8.141  65.651   1341
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.72 %
    Favored  : 81.93 %
  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:  0.27 (0.25), residues: 1154
  helix:  1.71 (0.23), residues: 528
  sheet: -0.09 (0.46), residues: 126
  loop : -1.48 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 134 
 HIS   0.003   0.001   HIS B  47 
 PHE   0.016   0.001   PHE A 209 
 TYR   0.016   0.002   TYR B 235 
 ARG   0.007   0.000   ARG B 271 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 117
  time to evaluate  : 1.008 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.6443 (m-10)
REVERT: B  109 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8146 (mmtt)
REVERT: B  150 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8099 (mt-10)
REVERT: B  152 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8517 (pm20)
REVERT: B  190 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8308 (mt-10)
REVERT: B  197 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8225 (tp30)
REVERT: B  427 MET cc_start: 0.8720 (mtm) cc_final: 0.8454 (mtm)
REVERT: B  475 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.7780 (mtp)
REVERT: B  530 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7637 (tt0)
REVERT: E   13 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.5797 (mtt)
REVERT: D   19 SER cc_start: 0.9023 (m) cc_final: 0.8729 (m)
REVERT: A   62 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7764 (tp30)
REVERT: A  144 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8350 (p)
REVERT: A  407 GLN cc_start: 0.7856 (mt0) cc_final: 0.7623 (mt0)
REVERT: A  422 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7534 (mtm-85)
REVERT: A  423 SER cc_start: 0.8737 (m) cc_final: 0.8170 (p)
REVERT: A  434 LYS cc_start: 0.8851 (mmtm) cc_final: 0.8418 (mmpt)
REVERT: A  435 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8034 (mm-30)
  outliers start: 33
  outliers final: 19
  residues processed: 135
  average time/residue: 1.5688
  time to fit residues: 223.2274
Evaluate side-chains
  143 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  109 LYS
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  152 GLN
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  423 MET
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain B residue  475 MET
Chi-restraints excluded: chain B residue  488 LYS
Chi-restraints excluded: chain B residue  519 GLU
Chi-restraints excluded: chain B residue  530 GLU
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   44 TYR
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain C residue   41 LEU
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  422 ARG
Chi-restraints excluded: chain A residue  435 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 66 optimal weight:    0.2980
   chunk 46 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    2.0186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.113758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.092889 restraints weight = 11369.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 1.68
r_work: 0.2773 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2652 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2643
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2643 r_free = 0.2643    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2643 r_free = 0.2643    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2643
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9457  Z= 0.293
  Angle     :  0.648   9.127  12787  Z= 0.344
  Chirality :  0.048   0.199   1428
  Planarity :  0.005   0.056   1619
  Dihedral  :  8.284  65.719   1341
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 14.72 %
    Favored  : 82.03 %
  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:  0.11 (0.25), residues: 1154
  helix:  1.55 (0.23), residues: 526
  sheet: -0.12 (0.46), residues: 126
  loop : -1.53 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 134 
 HIS   0.003   0.001   HIS B  47 
 PHE   0.018   0.002   PHE A 209 
 TYR   0.018   0.002   TYR B 235 
 ARG   0.006   0.000   ARG B 271 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 1.207 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.6494 (m-10)
REVERT: B  109 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8190 (mmtt)
REVERT: B  150 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8080 (mt-10)
REVERT: B  152 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8555 (pm20)
REVERT: B  197 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8220 (tp30)
REVERT: B  260 GLU cc_start: 0.8713 (tt0) cc_final: 0.8503 (tt0)
REVERT: B  427 MET cc_start: 0.8761 (mtm) cc_final: 0.8512 (mtm)
REVERT: B  436 LYS cc_start: 0.8381 (mtmm) cc_final: 0.7620 (mtpt)
REVERT: B  530 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7659 (tt0)
REVERT: E   13 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5812 (mtt)
REVERT: D   19 SER cc_start: 0.9082 (m) cc_final: 0.8804 (m)
REVERT: A   62 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7805 (tp30)
REVERT: A  144 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8395 (p)
REVERT: A  407 GLN cc_start: 0.7865 (mt0) cc_final: 0.7574 (mt0)
REVERT: A  422 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7533 (mtm-85)
REVERT: A  423 SER cc_start: 0.8753 (m) cc_final: 0.8196 (p)
REVERT: A  434 LYS cc_start: 0.8888 (mmtm) cc_final: 0.8445 (mmpt)
  outliers start: 32
  outliers final: 16
  residues processed: 130
  average time/residue: 1.7719
  time to fit residues: 243.0120
Evaluate side-chains
  138 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  109 LYS
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  152 GLN
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain B residue  530 GLU
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   44 TYR
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain C residue   41 LEU
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  422 ARG
Chi-restraints excluded: chain A residue  435 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 47 optimal weight:    0.0570
   chunk 52 optimal weight:    4.9990
   chunk 101 optimal weight:    0.8980
   chunk 103 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 107 optimal weight:    4.9990
   overall best weight:    1.3302

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.115972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.095220 restraints weight = 11479.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.2921 rms_B_bonded: 1.69
r_work: 0.2808 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2688 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2679
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2679 r_free = 0.2679    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2679 r_free = 0.2679    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2679
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9457  Z= 0.215
  Angle     :  0.588   7.427  12787  Z= 0.314
  Chirality :  0.046   0.195   1428
  Planarity :  0.005   0.053   1619
  Dihedral  :  8.033  65.568   1341
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 15.53 %
    Favored  : 82.03 %
  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:  0.26 (0.25), residues: 1154
  helix:  1.69 (0.23), residues: 528
  sheet: -0.02 (0.46), residues: 124
  loop : -1.50 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 134 
 HIS   0.003   0.001   HIS B  47 
 PHE   0.016   0.001   PHE A 209 
 TYR   0.015   0.002   TYR B 235 
 ARG   0.007   0.000   ARG B 271 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 1.118 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6464 (m-10)
REVERT: B  109 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8155 (mmtt)
REVERT: B  150 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8068 (mt-10)
REVERT: B  152 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8565 (pm20)
REVERT: B  190 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8324 (mt-10)
REVERT: B  197 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8218 (tp30)
REVERT: B  260 GLU cc_start: 0.8645 (tt0) cc_final: 0.8430 (tt0)
REVERT: B  427 MET cc_start: 0.8723 (mtm) cc_final: 0.8458 (mtm)
REVERT: B  530 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7629 (tt0)
REVERT: E   13 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.5826 (mtt)
REVERT: D   19 SER cc_start: 0.9041 (m) cc_final: 0.8756 (m)
REVERT: A   62 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7813 (tp30)
REVERT: A  144 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8363 (p)
REVERT: A  407 GLN cc_start: 0.7845 (mt0) cc_final: 0.7501 (mt0)
REVERT: A  423 SER cc_start: 0.8707 (m) cc_final: 0.8174 (p)
REVERT: A  434 LYS cc_start: 0.8902 (mmtm) cc_final: 0.8478 (mmpt)
REVERT: A  435 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8133 (mm-30)
  outliers start: 24
  outliers final: 15
  residues processed: 128
  average time/residue: 1.6202
  time to fit residues: 218.8311
Evaluate side-chains
  137 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  109 LYS
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  152 GLN
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  344 ASP
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain B residue  496 VAL
Chi-restraints excluded: chain B residue  530 GLU
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  435 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.113899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.093057 restraints weight = 11363.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 1.68
r_work: 0.2788 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2661
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2661 r_free = 0.2661    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2661 r_free = 0.2661    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2661
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9457  Z= 0.292
  Angle     :  0.643   9.530  12787  Z= 0.341
  Chirality :  0.048   0.199   1428
  Planarity :  0.005   0.055   1619
  Dihedral  :  8.068  65.509   1339
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.33 %
    Favored  : 82.03 %
  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:  0.13 (0.25), residues: 1154
  helix:  1.56 (0.23), residues: 528
  sheet: -0.13 (0.46), residues: 126
  loop : -1.51 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 134 
 HIS   0.003   0.001   HIS B  47 
 PHE   0.018   0.002   PHE A 209 
 TYR   0.018   0.002   TYR B 235 
 ARG   0.006   0.000   ARG B 271 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7991.96 seconds
wall clock time: 140 minutes 21.51 seconds (8421.51 seconds total)