Starting phenix.real_space_refine
on Fri Feb 14 14:30:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rw9_24711/02_2025/7rw9_24711.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rw9_24711/02_2025/7rw9_24711.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rw9_24711/02_2025/7rw9_24711.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rw9_24711/02_2025/7rw9_24711.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rw9_24711/02_2025/7rw9_24711.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rw9_24711/02_2025/7rw9_24711.cif"
  }
  resolution = 3.9
  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=   0.010
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: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    6691      2.51       5
     N    1781      2.21       5
     O    1851      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10365
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 613, 4516
          Classifications: {'peptide': 613}
          Incomplete info: {'truncation_to_alanine': 86}
          Link IDs: {'PTRANS': 22, 'TRANS': 590}
          Unresolved non-hydrogen bonds: 322
          Unresolved non-hydrogen angles: 383
          Unresolved non-hydrogen dihedrals: 265
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 16, 'ASN:plan1': 5, 'HIS:plan': 2, 'GLU:plan': 23, 'ARG:plan': 10}
          Unresolved non-hydrogen planarities: 219
    Chain: "B"
      Number of atoms: 3806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 567, 3806
          Classifications: {'peptide': 567}
          Incomplete info: {'truncation_to_alanine': 204}
          Link IDs: {'PTRANS': 26, 'TRANS': 540}
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 710
          Unresolved non-hydrogen angles: 881
          Unresolved non-hydrogen dihedrals: 571
          Unresolved non-hydrogen chiralities: 39
          Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 17, 'ASP:plan': 29, 'PHE:plan': 3, 'GLU:plan': 34, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 419
    Chain: "M"
      Number of atoms: 953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 953
          Classifications: {'peptide': 135}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          Unresolved non-hydrogen bonds: 143
          Unresolved non-hydrogen angles: 176
          Unresolved non-hydrogen dihedrals: 116
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 98
    Chain: "S"
      Number of atoms: 1090
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1090
          Classifications: {'peptide': 141}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'TRANS': 140}
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 71
  Time building chain proxies: 6.75, per 1000 atoms: 0.65
  Number of scatterers: 10365
  At special positions: 0
  Unit cell: (93.45, 100.57, 119.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1851      8.00
     N    1781      7.00
     C    6691      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.73
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2826

  Finding SS restraints...
    Secondary structure from input PDB file:
      88 helices and 5 sheets defined
      74.1% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 22
      removed outlier: 3.840A  pdb=" N   ALA A  14 " --> pdb=" O   MET A  10 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ASN A  22 " --> pdb=" O   SER A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 44
      removed outlier: 3.749A  pdb=" N   GLU A  29 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 69
      removed outlier: 3.652A  pdb=" N   GLY A  69 " --> pdb=" O   ILE A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 81
    Processing helix  chain 'A' and resid 82 through 84
      No H-bonds generated for 'chain 'A' and resid 82 through 84'
    Processing helix  chain 'A' and resid 87 through 101
    Processing helix  chain 'A' and resid 106 through 121
      removed outlier: 3.718A  pdb=" N   ALA A 121 " --> pdb=" O   LYS A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 138
      removed outlier: 3.746A  pdb=" N   MET A 128 " --> pdb=" O   ASN A 124 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   VAL A 138 " --> pdb=" O   CYS A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 147
    Processing helix  chain 'A' and resid 150 through 156
      removed outlier: 3.674A  pdb=" N   ILE A 154 " --> pdb=" O   GLU A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 179
    Processing helix  chain 'A' and resid 188 through 195
      removed outlier: 4.115A  pdb=" N   VAL A 192 " --> pdb=" O   TRP A 188 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL A 193 " --> pdb=" O   THR A 189 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   HIS A 194 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 198
      No H-bonds generated for 'chain 'A' and resid 196 through 198'
    Processing helix  chain 'A' and resid 201 through 218
    Processing helix  chain 'A' and resid 219 through 223
      removed outlier: 3.945A  pdb=" N   LYS A 223 " --> pdb=" O   GLU A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 238
      removed outlier: 4.575A  pdb=" N   LEU A 228 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR A 238 " --> pdb=" O   SER A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 246
      No H-bonds generated for 'chain 'A' and resid 244 through 246'
    Processing helix  chain 'A' and resid 254 through 267
      removed outlier: 3.681A  pdb=" N   CYS A 267 " --> pdb=" O   ARG A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 293
      removed outlier: 3.505A  pdb=" N   GLU A 293 " --> pdb=" O   ASN A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 321
      removed outlier: 3.689A  pdb=" N   SER A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 338
    Processing helix  chain 'A' and resid 342 through 357
    Processing helix  chain 'A' and resid 362 through 368
    Processing helix  chain 'A' and resid 369 through 380
    Processing helix  chain 'A' and resid 383 through 396
    Processing helix  chain 'A' and resid 401 through 415
    Processing helix  chain 'A' and resid 419 through 435
    Processing helix  chain 'A' and resid 438 through 453
      removed outlier: 3.823A  pdb=" N   TYR A 442 " --> pdb=" O   ASP A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 473
      removed outlier: 3.895A  pdb=" N   ASP A 473 " --> pdb=" O   VAL A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 488
      removed outlier: 3.672A  pdb=" N   GLN A 488 " --> pdb=" O   PHE A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 512
      removed outlier: 6.284A  pdb=" N   ASN A 509 " --> pdb=" O   GLY A 505 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   LEU A 510 " --> pdb=" O   GLU A 506 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   ILE A 511 " --> pdb=" O   PHE A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 517
    Processing helix  chain 'A' and resid 518 through 531
      removed outlier: 3.632A  pdb=" N   HIS A 531 " --> pdb=" O   HIS A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 552
    Processing helix  chain 'A' and resid 555 through 563
    Processing helix  chain 'A' and resid 565 through 570
    Processing helix  chain 'A' and resid 573 through 590
    Processing helix  chain 'A' and resid 593 through 599
      removed outlier: 3.576A  pdb=" N   LEU A 599 " --> pdb=" O   LEU A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 620
      removed outlier: 3.762A  pdb=" N   ALA A 614 " --> pdb=" O   SER A 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 23
    Processing helix  chain 'B' and resid 26 through 44
    Processing helix  chain 'B' and resid 47 through 49
      No H-bonds generated for 'chain 'B' and resid 47 through 49'
    Processing helix  chain 'B' and resid 50 through 58
    Processing helix  chain 'B' and resid 62 through 78
    Processing helix  chain 'B' and resid 82 through 85
    Processing helix  chain 'B' and resid 86 through 95
      removed outlier: 4.288A  pdb=" N   SER B  90 " --> pdb=" O   MET B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 112
      removed outlier: 3.646A  pdb=" N   ARG B 103 " --> pdb=" O   ASN B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 131
      removed outlier: 4.986A  pdb=" N   GLU B 124 " --> pdb=" O   GLU B 120 " (cutoff:3.500A)
      Proline residue:  B 125  - end of helix
      removed outlier: 4.230A  pdb=" N   LYS B 128 " --> pdb=" O   GLU B 124 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   CYS B 129 " --> pdb=" O   PRO B 125 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU B 130 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   LYS B 131 " --> pdb=" O   ARG B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 151
      removed outlier: 3.522A  pdb=" N   ASP B 150 " --> pdb=" O   ALA B 146 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   ILE B 151 " --> pdb=" O   LYS B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 168
      removed outlier: 4.057A  pdb=" N   GLY B 160 " --> pdb=" O   VAL B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 188
    Processing helix  chain 'B' and resid 200 through 214
    Processing helix  chain 'B' and resid 215 through 226
    Processing helix  chain 'B' and resid 227 through 229
      No H-bonds generated for 'chain 'B' and resid 227 through 229'
    Processing helix  chain 'B' and resid 233 through 245
      removed outlier: 3.567A  pdb=" N   ALA B 237 " --> pdb=" O   ASP B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 266
    Processing helix  chain 'B' and resid 276 through 284
    Processing helix  chain 'B' and resid 284 through 291
      removed outlier: 3.590A  pdb=" N   LEU B 288 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 294
      No H-bonds generated for 'chain 'B' and resid 292 through 294'
    Processing helix  chain 'B' and resid 295 through 313
    Processing helix  chain 'B' and resid 321 through 325
    Processing helix  chain 'B' and resid 331 through 346
    Processing helix  chain 'B' and resid 347 through 349
      No H-bonds generated for 'chain 'B' and resid 347 through 349'
    Processing helix  chain 'B' and resid 350 through 363
      removed outlier: 3.850A  pdb=" N   THR B 363 " --> pdb=" O   LYS B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 384
      removed outlier: 3.502A  pdb=" N   VAL B 384 " --> pdb=" O   CYS B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 401
    Processing helix  chain 'B' and resid 403 through 421
    Processing helix  chain 'B' and resid 425 through 427
      No H-bonds generated for 'chain 'B' and resid 425 through 427'
    Processing helix  chain 'B' and resid 428 through 435
      removed outlier: 3.645A  pdb=" N   ASN B 435 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 455
    Processing helix  chain 'B' and resid 461 through 470
    Processing helix  chain 'B' and resid 477 through 495
    Processing helix  chain 'B' and resid 496 through 498
      No H-bonds generated for 'chain 'B' and resid 496 through 498'
    Processing helix  chain 'B' and resid 499 through 513
      removed outlier: 4.000A  pdb=" N   VAL B 503 " --> pdb=" O   THR B 499 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASP B 513 " --> pdb=" O   LEU B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 531
      removed outlier: 3.801A  pdb=" N   LEU B 529 " --> pdb=" O   ILE B 525 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   SER B 531 " --> pdb=" O   TRP B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 533 through 542
    Processing helix  chain 'B' and resid 556 through 565
      removed outlier: 4.017A  pdb=" N   CYS B 565 " --> pdb=" O   ASP B 561 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 575
      removed outlier: 3.827A  pdb=" N   VAL B 573 " --> pdb=" O   SER B 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 577 through 581
      removed outlier: 3.518A  pdb=" N   PHE B 581 " --> pdb=" O   PRO B 578 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 25 through 36
      removed outlier: 3.863A  pdb=" N   VAL M  29 " --> pdb=" O   GLY M  25 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 74 through 94
    Processing helix  chain 'M' and resid 97 through 103
    Processing helix  chain 'M' and resid 104 through 115
    Processing helix  chain 'S' and resid 24 through 42
      removed outlier: 3.566A  pdb=" N   LYS S  28 " --> pdb=" O   ASP S  24 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLN S  29 " --> pdb=" O   ASP S  25 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL S  41 " --> pdb=" O   ALA S  37 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ARG S  42 " --> pdb=" O   VAL S  38 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 76 through 96
      removed outlier: 3.669A  pdb=" N   TYR S  80 " --> pdb=" O   ASN S  76 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 99 through 106
    Processing helix  chain 'S' and resid 106 through 117
    Processing helix  chain 'S' and resid 127 through 138
      removed outlier: 3.846A  pdb=" N   VAL S 131 " --> pdb=" O   SER S 127 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249
    Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 18
      removed outlier: 7.024A  pdb=" N   ILE M   7 " --> pdb=" O   LEU M  15 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   SER M  17 " --> pdb=" O   LEU M   5 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU M   5 " --> pdb=" O   SER M  17 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'M' and resid 116 through 117
      removed outlier: 3.811A  pdb=" N   ASP M 117 " --> pdb=" O   TYR M 120 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'S' and resid 14 through 19
      removed outlier: 6.400A  pdb=" N   ILE S   7 " --> pdb=" O   ARG S  15 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   ALA S  17 " --> pdb=" O   ILE S   5 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ILE S   5 " --> pdb=" O   ALA S  17 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   TRP S  19 " --> pdb=" O   ARG S   3 " (cutoff:3.500A)
      removed outlier: 8.275A  pdb=" N   ARG S   3 " --> pdb=" O   TRP S  19 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   CYS S  70 " --> pdb=" O   ARG S   3 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ILE S   5 " --> pdb=" O   CYS S  68 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   CYS S  68 " --> pdb=" O   ILE S   5 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ILE S   7 " --> pdb=" O   TYR S  66 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   TYR S  66 " --> pdb=" O   ILE S   7 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LYS S  56 " --> pdb=" O   VAL S  71 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL S  50 " --> pdb=" O   ILE S  57 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'S' and resid 118 through 119
      removed outlier: 3.673A  pdb=" N   LEU S 119 " --> pdb=" O   GLU S 122 " (cutoff:3.500A)

    710 hydrogen bonds defined for protein.
    2094 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: 3.56

  Time building geometry restraints manager: 3.12 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3397
        1.34 -     1.46: 2037
        1.46 -     1.58: 5045
        1.58 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 10540
  Sorted by residual:
  bond pdb=" CA  ASP B 340 "
       pdb=" C   ASP B 340 "
    ideal  model  delta    sigma   weight residual
    1.523  1.546 -0.023 1.35e-02 5.49e+03 2.81e+00
  bond pdb=" C   ASN B 200 "
       pdb=" N   PRO B 201 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.022 1.51e-02 4.39e+03 2.10e+00
  bond pdb=" C   ASP B 440 "
       pdb=" N   GLU B 441 "
    ideal  model  delta    sigma   weight residual
    1.330  1.349 -0.019 1.47e-02 4.63e+03 1.66e+00
  bond pdb=" CA  LYS A  24 "
       pdb=" C   LYS A  24 "
    ideal  model  delta    sigma   weight residual
    1.530  1.516  0.014 1.12e-02 7.97e+03 1.59e+00
  bond pdb=" CA  LEU B 248 "
       pdb=" CB  LEU B 248 "
    ideal  model  delta    sigma   weight residual
    1.524  1.542 -0.018 1.62e-02 3.81e+03 1.25e+00
  ... (remaining 10535 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 14061
        1.70 -     3.39: 302
        3.39 -     5.09: 54
        5.09 -     6.78: 12
        6.78 -     8.48: 5
  Bond angle restraints: 14434
  Sorted by residual:
  angle pdb=" N   ILE B 341 "
        pdb=" CA  ILE B 341 "
        pdb=" C   ILE B 341 "
      ideal   model   delta    sigma   weight residual
     110.72  103.76    6.96 1.01e+00 9.80e-01 4.75e+01
  angle pdb=" N   LEU B 339 "
        pdb=" CA  LEU B 339 "
        pdb=" C   LEU B 339 "
      ideal   model   delta    sigma   weight residual
     111.07  117.41   -6.34 1.07e+00 8.73e-01 3.51e+01
  angle pdb=" N   ILE B 341 "
        pdb=" CA  ILE B 341 "
        pdb=" CB  ILE B 341 "
      ideal   model   delta    sigma   weight residual
     110.58  117.76   -7.18 1.50e+00 4.44e-01 2.29e+01
  angle pdb=" C   ARG A 399 "
        pdb=" N   SER A 400 "
        pdb=" CA  SER A 400 "
      ideal   model   delta    sigma   weight residual
     121.54  128.31   -6.77 1.91e+00 2.74e-01 1.26e+01
  angle pdb=" N   SER A  25 "
        pdb=" CA  SER A  25 "
        pdb=" C   SER A  25 "
      ideal   model   delta    sigma   weight residual
     110.80  118.33   -7.53 2.13e+00 2.20e-01 1.25e+01
  ... (remaining 14429 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.45: 5802
       17.45 -    34.90: 415
       34.90 -    52.36: 67
       52.36 -    69.81: 10
       69.81 -    87.26: 10
  Dihedral angle restraints: 6304
    sinusoidal: 1976
      harmonic: 4328
  Sorted by residual:
  dihedral pdb=" CA  ARG A 399 "
           pdb=" C   ARG A 399 "
           pdb=" N   SER A 400 "
           pdb=" CA  SER A 400 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.56   34.44     0      5.00e+00 4.00e-02 4.74e+01
  dihedral pdb=" CA  CYS A 397 "
           pdb=" C   CYS A 397 "
           pdb=" N   ASP A 398 "
           pdb=" CA  ASP A 398 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.86   29.14     0      5.00e+00 4.00e-02 3.40e+01
  dihedral pdb=" CA  SER A 458 "
           pdb=" C   SER A 458 "
           pdb=" N   GLU A 459 "
           pdb=" CA  GLU A 459 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.55   25.45     0      5.00e+00 4.00e-02 2.59e+01
  ... (remaining 6301 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1481
       0.051 -    0.101: 301
       0.101 -    0.152: 42
       0.152 -    0.203: 2
       0.203 -    0.253: 2
  Chirality restraints: 1828
  Sorted by residual:
  chirality pdb=" CA  LEU B 339 "
            pdb=" N   LEU B 339 "
            pdb=" C   LEU B 339 "
            pdb=" CB  LEU B 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  SER A  25 "
            pdb=" N   SER A  25 "
            pdb=" C   SER A  25 "
            pdb=" CB  SER A  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  GLU S  93 "
            pdb=" N   GLU S  93 "
            pdb=" C   GLU S  93 "
            pdb=" CB  GLU S  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.83e-01
  ... (remaining 1825 not shown)

  Planarity restraints: 1823
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  58 "   -0.010 2.00e-02 2.50e+03   1.27e-02 3.23e+00
        pdb=" CG  TYR A  58 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  58 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  58 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  58 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  58 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  58 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A  58 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 603 "   -0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO A 604 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 604 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 604 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 217 "   -0.013 2.00e-02 2.50e+03   1.12e-02 3.14e+00
        pdb=" CG  TRP B 217 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 217 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 217 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 217 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 217 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 217 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 217 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 217 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 217 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1820 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 172
        2.69 -     3.24: 10656
        3.24 -     3.80: 15874
        3.80 -     4.35: 19203
        4.35 -     4.90: 32343
  Nonbonded interactions: 78248
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 398 "
            pdb=" OG1 THR B 401 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" O   ARG A 399 "
            pdb=" N   ASN A 401 "
     model   vdw
     2.160 3.120
  nonbonded pdb=" OH  TYR A 247 "
            pdb=" OE2 GLU S 125 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   HIS A 340 "
            pdb=" NH1 ARG A 346 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" O   PRO A 219 "
            pdb=" OH  TYR A 268 "
     model   vdw
     2.239 3.040
  ... (remaining 78243 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.640
  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:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     26.650
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10540  Z= 0.174
  Angle     :  0.628   8.476  14434  Z= 0.354
  Chirality :  0.041   0.253   1828
  Planarity :  0.003   0.045   1823
  Dihedral  : 13.176  87.262   3478
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  6.42 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.32 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  0.44 (0.23), residues: 1448
  helix:  1.28 (0.17), residues: 969
  sheet: -1.98 (0.74), residues: 46
  loop : -1.72 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 217 
 HIS   0.005   0.001   HIS A 200 
 PHE   0.022   0.001   PHE M 118 
 TYR   0.031   0.002   TYR A  58 
 ARG   0.007   0.000   ARG B 127 

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

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

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 1.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: M    1 MET cc_start: 0.6764 (mmt) cc_final: 0.6481 (mmt)
  outliers start: 1
  outliers final: 1
  residues processed: 142
  average time/residue: 0.2363
  time to fit residues: 47.2224
Evaluate side-chains
  84 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:    0.6980
   chunk 109 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0770
   chunk 58 optimal weight:    7.9990
   chunk 112 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 130 optimal weight:    3.9990
   overall best weight:    0.9140

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

Flipped N/Q/H residues before XYZ refinement:
A 369 HIS
A 403 GLN
B 305 ASN
S  36 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.071753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.056772 restraints weight = 52324.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.058433 restraints weight = 28335.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.059589 restraints weight = 19165.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10540  Z= 0.194
  Angle     :  0.606   9.441  14434  Z= 0.315
  Chirality :  0.039   0.167   1828
  Planarity :  0.003   0.032   1823
  Dihedral  :  4.704  41.309   1552
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.11 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  8.28 %
    Favored  : 90.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  0.88 (0.23), residues: 1448
  helix:  1.62 (0.17), residues: 985
  sheet: -1.38 (0.75), residues: 45
  loop : -1.75 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 462 
 HIS   0.003   0.001   HIS B 149 
 PHE   0.016   0.001   PHE M  81 
 TYR   0.024   0.001   TYR A  58 
 ARG   0.006   0.001   ARG S  10 

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

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

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 TYR cc_start: 0.8707 (m-10) cc_final: 0.7944 (m-80)
REVERT: S   49 PHE cc_start: 0.9012 (m-80) cc_final: 0.8184 (m-10)
REVERT: S   66 TYR cc_start: 0.7853 (m-10) cc_final: 0.7303 (m-10)
REVERT: S  125 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8055 (tm-30)
  outliers start: 10
  outliers final: 8
  residues processed: 100
  average time/residue: 0.1929
  time to fit residues: 29.6900
Evaluate side-chains
  85 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain B residue  144 CYS
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain M residue   23 ASP
Chi-restraints excluded: chain M residue   73 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 110 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 118 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 143 optimal weight:    0.9980
   chunk 131 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 109 optimal weight:    3.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
A  76 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.070950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.055898 restraints weight = 53254.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.057562 restraints weight = 28879.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.058431 restraints weight = 19410.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10540  Z= 0.185
  Angle     :  0.572   9.102  14434  Z= 0.295
  Chirality :  0.038   0.164   1828
  Planarity :  0.003   0.034   1823
  Dihedral  :  4.422  43.901   1550
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.04 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 10.72 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  1.11 (0.23), residues: 1448
  helix:  1.83 (0.17), residues: 971
  sheet: -1.04 (0.72), residues: 47
  loop : -1.68 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 462 
 HIS   0.004   0.001   HIS A 200 
 PHE   0.015   0.001   PHE M  81 
 TYR   0.017   0.001   TYR A 463 
 ARG   0.006   0.000   ARG S   3 

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

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

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 CYS cc_start: 0.8477 (m) cc_final: 0.8202 (m)
REVERT: B   56 ASN cc_start: 0.9331 (t0) cc_final: 0.9042 (m110)
REVERT: M    1 MET cc_start: 0.7193 (mmt) cc_final: 0.6792 (mmt)
REVERT: S   49 PHE cc_start: 0.9029 (m-80) cc_final: 0.8175 (m-10)
REVERT: S  125 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7998 (tm-30)
  outliers start: 14
  outliers final: 8
  residues processed: 94
  average time/residue: 0.2091
  time to fit residues: 30.3370
Evaluate side-chains
  87 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  485 GLU
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain M residue   23 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 122 optimal weight:    7.9990
   chunk 89 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3602 r_free = 0.3602 target = 0.070335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.055326 restraints weight = 52659.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.056981 restraints weight = 28653.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.058176 restraints weight = 19322.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10540  Z= 0.172
  Angle     :  0.549   9.950  14434  Z= 0.285
  Chirality :  0.038   0.154   1828
  Planarity :  0.003   0.034   1823
  Dihedral  :  4.330  45.363   1550
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  4.97 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.57 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  1.20 (0.23), residues: 1448
  helix:  1.88 (0.17), residues: 976
  sheet: -0.62 (0.75), residues: 47
  loop : -1.67 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 462 
 HIS   0.004   0.001   HIS A 200 
 PHE   0.020   0.001   PHE M 118 
 TYR   0.015   0.001   TYR A 463 
 ARG   0.004   0.000   ARG S  10 

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

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

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 CYS cc_start: 0.8499 (m) cc_final: 0.8230 (m)
REVERT: B   56 ASN cc_start: 0.9350 (t0) cc_final: 0.9089 (m-40)
REVERT: B   70 TYR cc_start: 0.9060 (m-10) cc_final: 0.8587 (m-80)
REVERT: S  125 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8009 (tm-30)
  outliers start: 16
  outliers final: 13
  residues processed: 97
  average time/residue: 0.2002
  time to fit residues: 29.7530
Evaluate side-chains
  90 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  485 GLU
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain M residue   23 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 125 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 13 optimal weight:    8.9990
   chunk 129 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 136 optimal weight:    0.2980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3606 r_free = 0.3606 target = 0.070670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.055668 restraints weight = 53012.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.057359 restraints weight = 28942.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.058572 restraints weight = 19583.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10540  Z= 0.159
  Angle     :  0.546  12.094  14434  Z= 0.279
  Chirality :  0.037   0.150   1828
  Planarity :  0.003   0.035   1823
  Dihedral  :  4.239  45.921   1550
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.04 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 12.74 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  1.34 (0.23), residues: 1448
  helix:  1.99 (0.17), residues: 972
  sheet: -0.33 (0.79), residues: 47
  loop : -1.64 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 462 
 HIS   0.004   0.001   HIS A 200 
 PHE   0.017   0.001   PHE S  87 
 TYR   0.013   0.001   TYR A 463 
 ARG   0.008   0.000   ARG S  10 

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

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

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 CYS cc_start: 0.8468 (m) cc_final: 0.8204 (m)
REVERT: B   56 ASN cc_start: 0.9357 (t0) cc_final: 0.9099 (m-40)
REVERT: B   70 TYR cc_start: 0.9051 (m-10) cc_final: 0.8535 (m-80)
REVERT: M   65 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8084 (tt)
REVERT: S  125 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7984 (tm-30)
  outliers start: 21
  outliers final: 13
  residues processed: 103
  average time/residue: 0.1999
  time to fit residues: 31.2439
Evaluate side-chains
  89 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  485 GLU
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain M residue   23 ASP
Chi-restraints excluded: chain M residue   65 LEU
Chi-restraints excluded: chain S residue  115 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 108 optimal weight:    0.7980
   chunk 102 optimal weight:    0.6980
   chunk 62 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0570
   chunk 106 optimal weight:    3.9990
   chunk 114 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    0.6698

-------------------------------------------------------------------------------
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 = 0.3599 r_free = 0.3599 target = 0.070321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.055370 restraints weight = 53326.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.057061 restraints weight = 28975.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.058279 restraints weight = 19493.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10540  Z= 0.152
  Angle     :  0.548  11.711  14434  Z= 0.278
  Chirality :  0.037   0.152   1828
  Planarity :  0.003   0.036   1823
  Dihedral  :  4.220  45.630   1550
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  4.77 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 13.59 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  1.40 (0.23), residues: 1448
  helix:  2.04 (0.17), residues: 972
  sheet: -0.06 (0.80), residues: 45
  loop : -1.65 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 462 
 HIS   0.004   0.001   HIS A 200 
 PHE   0.021   0.001   PHE M  81 
 TYR   0.012   0.001   TYR S  80 
 ARG   0.008   0.000   ARG S  42 

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

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

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 1.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 CYS cc_start: 0.8466 (m) cc_final: 0.8201 (m)
REVERT: A  183 VAL cc_start: 0.7646 (OUTLIER) cc_final: 0.7328 (p)
REVERT: B   56 ASN cc_start: 0.9346 (t0) cc_final: 0.9095 (m-40)
REVERT: B   70 TYR cc_start: 0.9087 (m-10) cc_final: 0.8575 (m-80)
REVERT: S   42 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7627 (mtp85)
REVERT: S  125 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7938 (tm-30)
  outliers start: 23
  outliers final: 18
  residues processed: 106
  average time/residue: 0.1947
  time to fit residues: 31.4312
Evaluate side-chains
  96 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  485 GLU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain M residue   23 ASP
Chi-restraints excluded: chain M residue   63 ILE
Chi-restraints excluded: chain M residue   92 TYR
Chi-restraints excluded: chain S residue    6 LEU
Chi-restraints excluded: chain S residue  115 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 76 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 1 optimal weight:    8.9990
   chunk 96 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 3 optimal weight:    9.9990
   chunk 105 optimal weight:    4.9990
   chunk 113 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3601 r_free = 0.3601 target = 0.071698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.055124 restraints weight = 52907.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.056854 restraints weight = 28690.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.058142 restraints weight = 19541.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10540  Z= 0.166
  Angle     :  0.557  11.803  14434  Z= 0.282
  Chirality :  0.038   0.199   1828
  Planarity :  0.003   0.036   1823
  Dihedral  :  4.193  45.439   1550
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  4.63 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.01 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  1.46 (0.23), residues: 1448
  helix:  2.07 (0.17), residues: 972
  sheet: -0.31 (0.76), residues: 47
  loop : -1.53 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 462 
 HIS   0.004   0.001   HIS A 200 
 PHE   0.018   0.001   PHE S  87 
 TYR   0.013   0.001   TYR A 418 
 ARG   0.007   0.000   ARG S  42 

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

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

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 1.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 CYS cc_start: 0.8485 (m) cc_final: 0.8220 (m)
REVERT: A  183 VAL cc_start: 0.7711 (OUTLIER) cc_final: 0.7416 (p)
REVERT: A  412 TYR cc_start: 0.8835 (t80) cc_final: 0.8617 (t80)
REVERT: B   56 ASN cc_start: 0.9375 (t0) cc_final: 0.9157 (m-40)
REVERT: B   70 TYR cc_start: 0.9099 (m-10) cc_final: 0.8606 (m-80)
REVERT: S   42 ARG cc_start: 0.8008 (mtp85) cc_final: 0.7574 (mtp85)
REVERT: S  125 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7896 (tm-30)
  outliers start: 26
  outliers final: 18
  residues processed: 107
  average time/residue: 0.1928
  time to fit residues: 31.1625
Evaluate side-chains
  98 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  485 GLU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain M residue   23 ASP
Chi-restraints excluded: chain M residue   63 ILE
Chi-restraints excluded: chain S residue    6 LEU
Chi-restraints excluded: chain S residue  115 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 124 optimal weight:    0.8980
   chunk 98 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 67 optimal weight:   20.0000
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3591 r_free = 0.3591 target = 0.069735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.054856 restraints weight = 53523.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.056518 restraints weight = 29183.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.057663 restraints weight = 19735.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10540  Z= 0.171
  Angle     :  0.560  12.027  14434  Z= 0.285
  Chirality :  0.038   0.195   1828
  Planarity :  0.003   0.036   1823
  Dihedral  :  4.181  45.437   1550
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  4.70 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 14.65 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 (0.23), residues: 1448
  helix:  2.08 (0.17), residues: 973
  sheet: -0.41 (0.74), residues: 47
  loop : -1.52 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 462 
 HIS   0.004   0.001   HIS A 200 
 PHE   0.014   0.001   PHE S  67 
 TYR   0.026   0.001   TYR M  20 
 ARG   0.006   0.000   ARG S  42 

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

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

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 86
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 CYS cc_start: 0.8461 (m) cc_final: 0.8198 (m)
REVERT: A  183 VAL cc_start: 0.7628 (OUTLIER) cc_final: 0.7333 (p)
REVERT: A  412 TYR cc_start: 0.8826 (t80) cc_final: 0.8614 (t80)
REVERT: B   56 ASN cc_start: 0.9365 (t0) cc_final: 0.9162 (m-40)
REVERT: B   70 TYR cc_start: 0.9132 (m-10) cc_final: 0.8612 (m-80)
REVERT: S   42 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7591 (mtp85)
REVERT: S  125 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7982 (tm-30)
  outliers start: 23
  outliers final: 19
  residues processed: 104
  average time/residue: 0.2067
  time to fit residues: 32.0284
Evaluate side-chains
  100 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 1.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  485 GLU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain M residue   23 ASP
Chi-restraints excluded: chain M residue   63 ILE
Chi-restraints excluded: chain S residue    6 LEU
Chi-restraints excluded: chain S residue  115 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 61 optimal weight:   40.0000
   chunk 38 optimal weight:    0.8980
   chunk 106 optimal weight:    4.9990
   chunk 114 optimal weight:    0.6980
   chunk 113 optimal weight:    0.2980
   chunk 67 optimal weight:   20.0000
   chunk 43 optimal weight:    4.9990
   chunk 64 optimal weight:   30.0000
   chunk 143 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.7784

-------------------------------------------------------------------------------
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 = 0.3542 r_free = 0.3542 target = 0.067692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.052600 restraints weight = 54430.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.054181 restraints weight = 29840.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.055326 restraints weight = 20369.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10540  Z= 0.260
  Angle     :  0.602  11.820  14434  Z= 0.312
  Chirality :  0.039   0.192   1828
  Planarity :  0.003   0.035   1823
  Dihedral  :  4.396  46.441   1550
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.04 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.18 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  1.39 (0.23), residues: 1448
  helix:  1.97 (0.17), residues: 981
  sheet: -0.54 (0.73), residues: 47
  loop : -1.51 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 462 
 HIS   0.003   0.001   HIS A 200 
 PHE   0.030   0.002   PHE S 107 
 TYR   0.011   0.001   TYR A 418 
 ARG   0.006   0.000   ARG S  42 

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

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

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 1.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7670 (p)
REVERT: A  185 MET cc_start: 0.8584 (mmp) cc_final: 0.8384 (mmp)
REVERT: A  412 TYR cc_start: 0.8918 (t80) cc_final: 0.8714 (t80)
REVERT: B   70 TYR cc_start: 0.9093 (m-10) cc_final: 0.8633 (m-80)
REVERT: S    3 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8369 (tpp80)
REVERT: S  125 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7995 (tm-30)
  outliers start: 22
  outliers final: 18
  residues processed: 98
  average time/residue: 0.2065
  time to fit residues: 30.2364
Evaluate side-chains
  96 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  485 GLU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain M residue    2 ILE
Chi-restraints excluded: chain M residue   23 ASP
Chi-restraints excluded: chain M residue   63 ILE
Chi-restraints excluded: chain S residue    3 ARG
Chi-restraints excluded: chain S residue    6 LEU
Chi-restraints excluded: chain S residue  115 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 6 optimal weight:    0.0370
   chunk 111 optimal weight:    0.9990
   chunk 134 optimal weight:    0.3980
   chunk 123 optimal weight:    2.9990
   chunk 132 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 120 optimal weight:    0.9990
   chunk 110 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 129 optimal weight:    4.9990
   overall best weight:    0.6862

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

Flipped N/Q/H residues before XYZ refinement:
B  56 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.069237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.054267 restraints weight = 53516.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.055912 restraints weight = 29207.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.057120 restraints weight = 19810.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10540  Z= 0.160
  Angle     :  0.594  18.099  14434  Z= 0.296
  Chirality :  0.038   0.194   1828
  Planarity :  0.003   0.036   1823
  Dihedral  :  4.240  45.683   1550
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  4.70 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.92 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  1.42 (0.23), residues: 1448
  helix:  2.01 (0.17), residues: 976
  sheet: -0.50 (0.74), residues: 47
  loop : -1.51 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 462 
 HIS   0.004   0.001   HIS A 200 
 PHE   0.026   0.001   PHE M  81 
 TYR   0.011   0.001   TYR A 463 
 ARG   0.004   0.000   ARG S  10 

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

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

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2896 Ramachandran restraints generated.
    1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 1.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 CYS cc_start: 0.8557 (m) cc_final: 0.8284 (m)
REVERT: A  183 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7621 (p)
REVERT: B   70 TYR cc_start: 0.9171 (m-10) cc_final: 0.8597 (m-80)
REVERT: S  125 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7968 (tm-30)
  outliers start: 20
  outliers final: 16
  residues processed: 102
  average time/residue: 0.1898
  time to fit residues: 29.9376
Evaluate side-chains
  95 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  485 GLU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain M residue    2 ILE
Chi-restraints excluded: chain M residue   23 ASP
Chi-restraints excluded: chain M residue   63 ILE
Chi-restraints excluded: chain S residue    6 LEU
Chi-restraints excluded: chain S residue  115 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 128 optimal weight:    4.9990
   chunk 121 optimal weight:    4.9990
   chunk 87 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 75 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   chunk 134 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9980
   chunk 140 optimal weight:    4.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
B  56 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.069525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.052909 restraints weight = 52967.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.054548 restraints weight = 29119.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.055770 restraints weight = 20032.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10540  Z= 0.246
  Angle     :  0.615  14.628  14434  Z= 0.315
  Chirality :  0.039   0.194   1828
  Planarity :  0.003   0.034   1823
  Dihedral  :  4.393  46.325   1550
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  4.77 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.35 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  1.37 (0.23), residues: 1448
  helix:  1.94 (0.17), residues: 981
  sheet: -1.07 (0.68), residues: 55
  loop : -1.37 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 462 
 HIS   0.003   0.001   HIS A 200 
 PHE   0.026   0.002   PHE S 107 
 TYR   0.013   0.001   TYR A 418 
 ARG   0.005   0.000   ARG S  42 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2868.15 seconds
wall clock time: 52 minutes 25.16 seconds (3145.16 seconds total)