Starting phenix.real_space_refine
on Thu Mar 13 12:47:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tss_41600/03_2025/8tss_41600.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tss_41600/03_2025/8tss_41600.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tss_41600/03_2025/8tss_41600.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tss_41600/03_2025/8tss_41600.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tss_41600/03_2025/8tss_41600.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tss_41600/03_2025/8tss_41600.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.042
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      54      5.16       5
     C    5652      2.51       5
     N    1552      2.21       5
     O    1660      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8918
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4459
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 575, 4459
          Classifications: {'peptide': 575}
          Link IDs: {'PTRANS': 13, 'TRANS': 561}
    Chain: "B"
      Number of atoms: 4459
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 575, 4459
          Classifications: {'peptide': 575}
          Link IDs: {'PTRANS': 13, 'TRANS': 561}
  Time building chain proxies: 5.88, per 1000 atoms: 0.66
  Number of scatterers: 8918
  At special positions: 0
  Unit cell: (67.095, 135.255, 136.32, 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      54     16.00
     O    1660      8.00
     N    1552      7.00
     C    5652      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: 2.42
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 4 sheets defined
      70.5% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 21
      Proline residue:  A  18  - end of helix
    Processing helix  chain 'A' and resid 23 through 48
      removed outlier: 3.692A  pdb=" N   LEU A  27 " --> pdb=" O   PHE A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 66
    Processing helix  chain 'A' and resid 66 through 109
    Processing helix  chain 'A' and resid 112 through 119
      removed outlier: 4.322A  pdb=" N   PHE A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 164
      removed outlier: 4.029A  pdb=" N   ASP A 131 " --> pdb=" O   ARG A 127 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   SER A 132 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLY A 150 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 209
      removed outlier: 3.715A  pdb=" N   SER A 168 " --> pdb=" O   SER A 164 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ILE A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
      removed outlier: 4.020A  pdb=" N   THR A 199 " --> pdb=" O   ASN A 195 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLN A 202 " --> pdb=" O   ASN A 198 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   THR A 205 " --> pdb=" O   GLY A 201 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA A 207 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLN A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 212
      No H-bonds generated for 'chain 'A' and resid 210 through 212'
    Processing helix  chain 'A' and resid 213 through 221
      removed outlier: 3.787A  pdb=" N   LEU A 218 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   ILE A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   PHE A 220 " --> pdb=" O   GLU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 272
      removed outlier: 4.439A  pdb=" N   ASP A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
    Processing helix  chain 'A' and resid 275 through 280
      removed outlier: 5.710A  pdb=" N   THR A 280 " --> pdb=" O   ASP A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 323
      removed outlier: 4.064A  pdb=" N   THR A 285 " --> pdb=" O   ALA A 281 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 3.587A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   ASN A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLN A 309 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ARG A 310 " --> pdb=" O   ALA A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 390
      removed outlier: 3.584A  pdb=" N   THR A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 418
    Processing helix  chain 'A' and resid 432 through 438
      removed outlier: 3.750A  pdb=" N   ALA A 438 " --> pdb=" O   ALA A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 464
    Processing helix  chain 'A' and resid 468 through 472
    Processing helix  chain 'A' and resid 482 through 497
    Processing helix  chain 'A' and resid 515 through 527
    Processing helix  chain 'A' and resid 538 through 545
      removed outlier: 3.781A  pdb=" N   ILE A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 569
    Processing helix  chain 'A' and resid 570 through 578
      removed outlier: 3.652A  pdb=" N   MET A 578 " --> pdb=" O   GLN A 574 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 21
      Proline residue:  B  18  - end of helix
    Processing helix  chain 'B' and resid 23 through 53
      removed outlier: 3.695A  pdb=" N   LEU B  27 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   LYS B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 61 through 66
    Processing helix  chain 'B' and resid 66 through 109
    Processing helix  chain 'B' and resid 112 through 119
      removed outlier: 4.234A  pdb=" N   PHE B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 164
      removed outlier: 4.001A  pdb=" N   ASP B 131 " --> pdb=" O   ARG B 127 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   SER B 132 " --> pdb=" O   ILE B 128 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLY B 150 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 209
      Proline residue:  B 176  - end of helix
      removed outlier: 4.029A  pdb=" N   THR B 199 " --> pdb=" O   ASN B 195 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   GLN B 202 " --> pdb=" O   ASN B 198 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   THR B 205 " --> pdb=" O   GLY B 201 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLN B 209 " --> pdb=" O   THR B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
      removed outlier: 3.551A  pdb=" N   LEU B 218 " --> pdb=" O   HIS B 214 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   ILE B 219 " --> pdb=" O   LYS B 215 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE B 220 " --> pdb=" O   GLU B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 272
      removed outlier: 4.328A  pdb=" N   ASP B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      Proline residue:  B 253  - end of helix
    Processing helix  chain 'B' and resid 272 through 277
      removed outlier: 3.579A  pdb=" N   ASP B 277 " --> pdb=" O   PRO B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 280
      No H-bonds generated for 'chain 'B' and resid 278 through 280'
    Processing helix  chain 'B' and resid 281 through 323
      removed outlier: 4.084A  pdb=" N   THR B 285 " --> pdb=" O   ALA B 281 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER B 290 " --> pdb=" O   VAL B 286 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   ARG B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
      removed outlier: 3.568A  pdb=" N   THR B 302 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   ASN B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLN B 309 " --> pdb=" O   ASN B 305 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ARG B 310 " --> pdb=" O   ALA B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 390
      removed outlier: 3.703A  pdb=" N   THR B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 418
    Processing helix  chain 'B' and resid 432 through 438
      removed outlier: 3.871A  pdb=" N   ALA B 438 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 459 through 464
      removed outlier: 3.569A  pdb=" N   ASN B 464 " --> pdb=" O   MET B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 472
    Processing helix  chain 'B' and resid 482 through 497
      removed outlier: 3.529A  pdb=" N   ARG B 497 " --> pdb=" O   ARG B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 515 through 527
    Processing helix  chain 'B' and resid 538 through 545
      removed outlier: 3.626A  pdb=" N   ILE B 542 " --> pdb=" O   ARG B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 561 through 569
    Processing helix  chain 'B' and resid 570 through 578
      removed outlier: 3.738A  pdb=" N   MET B 578 " --> pdb=" O   GLN B 574 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 365
      removed outlier: 5.540A  pdb=" N   VAL A 347 " --> pdb=" O   ASN A 361 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ASN A 363 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ARG A 345 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   LYS A 365 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   GLU A 343 " --> pdb=" O   LYS A 365 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   PHE A 344 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   LEU A 401 " --> pdb=" O   PHE A 344 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   ASN A 346 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   GLU A 399 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 423
      removed outlier: 6.494A  pdb=" N   ALA A 420 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   ASP A 505 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   VAL A 422 " --> pdb=" O   ASP A 505 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   LEU A 502 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   ILE A 535 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   LEU A 504 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   VAL A 551 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 5.809A  pdb=" N   VAL A 375 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   GLU A 552 " --> pdb=" O   ILE A 556 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   ILE A 556 " --> pdb=" O   GLU A 552 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 359 through 365
      removed outlier: 5.524A  pdb=" N   VAL B 347 " --> pdb=" O   ASN B 361 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   ASN B 363 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ARG B 345 " --> pdb=" O   ASN B 363 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   LYS B 365 " --> pdb=" O   GLU B 343 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   GLU B 343 " --> pdb=" O   LYS B 365 " (cutoff:3.500A)
      removed outlier: 5.419A  pdb=" N   PHE B 344 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   LEU B 401 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   ASN B 346 " --> pdb=" O   GLU B 399 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   GLU B 399 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 423
      removed outlier: 6.805A  pdb=" N   ALA B 420 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   ASP B 505 " --> pdb=" O   ALA B 420 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   VAL B 422 " --> pdb=" O   ASP B 505 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   THR B 371 " --> pdb=" O   GLU B 547 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   VAL B 549 " --> pdb=" O   THR B 371 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   VAL B 551 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   VAL B 375 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLU B 558 " --> pdb=" O   VAL B 550 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   GLU B 552 " --> pdb=" O   ILE B 556 " (cutoff:3.500A)
      removed outlier: 4.901A  pdb=" N   ILE B 556 " --> pdb=" O   GLU B 552 " (cutoff:3.500A)

    575 hydrogen bonds defined for protein.
    1689 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.56

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2956
        1.35 -     1.46: 1945
        1.46 -     1.58: 4045
        1.58 -     1.70: 0
        1.70 -     1.82: 104
  Bond restraints: 9050
  Sorted by residual:
  bond pdb=" N   LEU A 279 "
       pdb=" CA  LEU A 279 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.19e-02 7.06e+03 7.16e+00
  bond pdb=" N   ILE A 389 "
       pdb=" CA  ILE A 389 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.032 1.19e-02 7.06e+03 7.15e+00
  bond pdb=" N   SER A 278 "
       pdb=" CA  SER A 278 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.10e-02 8.26e+03 6.93e+00
  bond pdb=" N   LEU A 388 "
       pdb=" CA  LEU A 388 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.029 1.21e-02 6.83e+03 5.91e+00
  bond pdb=" N   SER A 387 "
       pdb=" CA  SER A 387 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.23e-02 6.61e+03 4.91e+00
  ... (remaining 9045 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 12005
        2.25 -     4.51: 181
        4.51 -     6.76: 31
        6.76 -     9.02: 5
        9.02 -    11.27: 8
  Bond angle restraints: 12230
  Sorted by residual:
  angle pdb=" CA  ARG B 190 "
        pdb=" CB  ARG B 190 "
        pdb=" CG  ARG B 190 "
      ideal   model   delta    sigma   weight residual
     114.10  121.65   -7.55 2.00e+00 2.50e-01 1.43e+01
  angle pdb=" CB  MET A 276 "
        pdb=" CG  MET A 276 "
        pdb=" SD  MET A 276 "
      ideal   model   delta    sigma   weight residual
     112.70  123.97  -11.27 3.00e+00 1.11e-01 1.41e+01
  angle pdb=" CB  MET A 100 "
        pdb=" CG  MET A 100 "
        pdb=" SD  MET A 100 "
      ideal   model   delta    sigma   weight residual
     112.70  123.64  -10.94 3.00e+00 1.11e-01 1.33e+01
  angle pdb=" CB  MET B 100 "
        pdb=" CG  MET B 100 "
        pdb=" SD  MET B 100 "
      ideal   model   delta    sigma   weight residual
     112.70  123.44  -10.74 3.00e+00 1.11e-01 1.28e+01
  angle pdb=" CB  MET B 456 "
        pdb=" CG  MET B 456 "
        pdb=" SD  MET B 456 "
      ideal   model   delta    sigma   weight residual
     112.70  123.29  -10.59 3.00e+00 1.11e-01 1.25e+01
  ... (remaining 12225 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.05: 4594
       14.05 -    28.11: 598
       28.11 -    42.16: 228
       42.16 -    56.21: 47
       56.21 -    70.26: 37
  Dihedral angle restraints: 5504
    sinusoidal: 2182
      harmonic: 3322
  Sorted by residual:
  dihedral pdb=" CA  GLN B 209 "
           pdb=" C   GLN B 209 "
           pdb=" N   MET B 210 "
           pdb=" CA  MET B 210 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.34   23.66     0      5.00e+00 4.00e-02 2.24e+01
  dihedral pdb=" CA  THR A 199 "
           pdb=" C   THR A 199 "
           pdb=" N   MET A 200 "
           pdb=" CA  MET A 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.00   19.00     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  SER A 251 "
           pdb=" C   SER A 251 "
           pdb=" N   ASP A 252 "
           pdb=" CA  ASP A 252 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.92  -16.08     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 5501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1058
       0.042 -    0.084: 289
       0.084 -    0.127: 94
       0.127 -    0.169: 11
       0.169 -    0.211: 2
  Chirality restraints: 1454
  Sorted by residual:
  chirality pdb=" CA  ILE A 389 "
            pdb=" N   ILE A 389 "
            pdb=" C   ILE A 389 "
            pdb=" CB  ILE A 389 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CB  VAL B 375 "
            pdb=" CA  VAL B 375 "
            pdb=" CG1 VAL B 375 "
            pdb=" CG2 VAL B 375 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.09e-01
  chirality pdb=" CG  LEU B 279 "
            pdb=" CB  LEU B 279 "
            pdb=" CD1 LEU B 279 "
            pdb=" CD2 LEU B 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.04e-01
  ... (remaining 1451 not shown)

  Planarity restraints: 1548
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 111 "   -0.051 5.00e-02 4.00e+02   7.67e-02 9.41e+00
        pdb=" N   PRO A 112 "    0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A 112 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 112 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 272 "    0.047 5.00e-02 4.00e+02   7.15e-02 8.18e+00
        pdb=" N   PRO B 273 "   -0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO B 273 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 273 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 499 "    0.035 5.00e-02 4.00e+02   5.30e-02 4.49e+00
        pdb=" N   PRO B 500 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 500 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 500 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1545 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1837
        2.78 -     3.31: 9610
        3.31 -     3.84: 15224
        3.84 -     4.37: 16731
        4.37 -     4.90: 28103
  Nonbonded interactions: 71505
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 467 "
            pdb=" OG1 THR A 472 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   LEU A 526 "
            pdb=" NH1 ARG A 530 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" O   LEU B 526 "
            pdb=" NH1 ARG B 530 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" OG  SER B 380 "
            pdb=" OE1 GLU B 552 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" ND1 HIS B 562 "
            pdb=" OH  TYR B 572 "
     model   vdw
     2.271 3.120
  ... (remaining 71500 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.670
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     23.870
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
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      :  0.004   0.056   9050  Z= 0.241
  Angle     :  0.750  11.275  12230  Z= 0.399
  Chirality :  0.043   0.211   1454
  Planarity :  0.006   0.077   1548
  Dihedral  : 15.891  70.263   3356
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.45 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 23.93 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.24), residues: 1146
  helix:  0.91 (0.19), residues: 728
  sheet:  0.15 (0.77), residues: 54
  loop : -1.14 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  66 
 HIS   0.015   0.001   HIS A 214 
 PHE   0.026   0.002   PHE A 116 
 TYR   0.019   0.001   TYR B 439 
 ARG   0.014   0.001   ARG B 190 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 135
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.7530 (t70) cc_final: 0.7271 (t70)
REVERT: B  107 HIS cc_start: 0.7834 (t70) cc_final: 0.7464 (t70)
REVERT: B  210 MET cc_start: 0.6669 (mtm) cc_final: 0.6283 (mtm)
  outliers start: 4
  outliers final: 3
  residues processed: 138
  average time/residue: 0.2099
  time to fit residues: 41.4393
Evaluate side-chains
  129 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 126
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  502 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:   20.0000
   chunk 86 optimal weight:    0.7980
   chunk 47 optimal weight:   10.0000
   chunk 29 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 89 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 103 optimal weight:    0.0770
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.195211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.138028 restraints weight = 10877.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.140138 restraints weight = 6577.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.141260 restraints weight = 5387.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.1230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9050  Z= 0.207
  Angle     :  0.611   8.032  12230  Z= 0.318
  Chirality :  0.041   0.149   1454
  Planarity :  0.005   0.059   1548
  Dihedral  :  4.605  50.914   1257
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 20.45 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.25), residues: 1146
  helix:  1.40 (0.19), residues: 754
  sheet:  0.17 (0.75), residues: 54
  loop : -1.32 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  66 
 HIS   0.018   0.002   HIS A 214 
 PHE   0.015   0.002   PHE B 429 
 TYR   0.011   0.001   TYR B 439 
 ARG   0.006   0.000   ARG B 190 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 145
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.7954 (t70) cc_final: 0.7551 (t70)
REVERT: A  408 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7960 (mpt180)
REVERT: A  578 MET cc_start: 0.6149 (pmm) cc_final: 0.5903 (pmm)
REVERT: B  107 HIS cc_start: 0.8113 (t70) cc_final: 0.7718 (t70)
  outliers start: 42
  outliers final: 20
  residues processed: 174
  average time/residue: 0.1925
  time to fit residues: 47.1168
Evaluate side-chains
  149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  562 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 54 optimal weight:    9.9990
   chunk 88 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 104 optimal weight:    9.9990
   chunk 47 optimal weight:    8.9990
   chunk 79 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 537 HIS
B 195 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.191292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.131999 restraints weight = 11228.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.134761 restraints weight = 7575.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.134977 restraints weight = 5833.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9050  Z= 0.276
  Angle     :  0.652   7.832  12230  Z= 0.334
  Chirality :  0.042   0.173   1454
  Planarity :  0.004   0.057   1548
  Dihedral  :  3.899  21.219   1250
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 20.04 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.25), residues: 1146
  helix:  1.34 (0.19), residues: 762
  sheet:  0.38 (0.79), residues: 44
  loop : -1.33 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  66 
 HIS   0.012   0.001   HIS A 214 
 PHE   0.026   0.002   PHE A 429 
 TYR   0.014   0.002   TYR A 439 
 ARG   0.004   0.000   ARG B 538 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 137
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.8073 (t70) cc_final: 0.7567 (t70)
REVERT: A  210 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.6197 (ttm)
REVERT: A  309 GLN cc_start: 0.6431 (OUTLIER) cc_final: 0.6140 (tt0)
REVERT: A  388 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8609 (mp)
REVERT: A  578 MET cc_start: 0.6370 (pmm) cc_final: 0.6163 (pmm)
REVERT: B  107 HIS cc_start: 0.8244 (t70) cc_final: 0.7760 (t70)
REVERT: B  250 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7214 (tp)
REVERT: B  309 GLN cc_start: 0.6387 (OUTLIER) cc_final: 0.6044 (tt0)
REVERT: B  460 MET cc_start: 0.7045 (mmm) cc_final: 0.6759 (mmm)
REVERT: B  537 HIS cc_start: 0.6256 (t-170) cc_final: 0.5910 (t-170)
REVERT: B  578 MET cc_start: 0.5164 (pmm) cc_final: 0.4842 (pmm)
  outliers start: 57
  outliers final: 34
  residues processed: 176
  average time/residue: 0.1762
  time to fit residues: 45.2821
Evaluate side-chains
  168 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 129
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  309 GLN
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  309 GLN
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  562 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 91 optimal weight:    7.9990
   chunk 67 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   chunk 111 optimal weight:    4.9990
   chunk 110 optimal weight:   20.0000
   chunk 78 optimal weight:    0.5980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 214 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.192528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.136008 restraints weight = 11140.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.135001 restraints weight = 8041.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.137081 restraints weight = 7378.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9050  Z= 0.212
  Angle     :  0.604   8.723  12230  Z= 0.309
  Chirality :  0.041   0.135   1454
  Planarity :  0.004   0.047   1548
  Dihedral  :  3.848  20.839   1250
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 22.39 %
    Favored  : 72.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.25), residues: 1146
  helix:  1.49 (0.19), residues: 754
  sheet:  0.25 (0.78), residues: 44
  loop : -1.12 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  66 
 HIS   0.011   0.001   HIS A 214 
 PHE   0.025   0.002   PHE A 429 
 TYR   0.018   0.001   TYR A 130 
 ARG   0.003   0.000   ARG A 102 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 141
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.8001 (t70) cc_final: 0.7471 (t70)
REVERT: A  210 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.6005 (ttm)
REVERT: A  216 GLU cc_start: 0.8699 (tp30) cc_final: 0.8370 (tp30)
REVERT: A  309 GLN cc_start: 0.6464 (OUTLIER) cc_final: 0.5997 (tt0)
REVERT: A  388 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8667 (mp)
REVERT: B  107 HIS cc_start: 0.8150 (t70) cc_final: 0.7713 (t70)
REVERT: B  250 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7265 (tp)
REVERT: B  309 GLN cc_start: 0.6417 (OUTLIER) cc_final: 0.5958 (tt0)
REVERT: B  395 ILE cc_start: 0.6443 (OUTLIER) cc_final: 0.5760 (tp)
REVERT: B  495 LEU cc_start: 0.8820 (mm) cc_final: 0.8468 (mm)
REVERT: B  537 HIS cc_start: 0.6581 (t-170) cc_final: 0.6275 (t-90)
REVERT: B  578 MET cc_start: 0.5221 (pmm) cc_final: 0.4987 (pmm)
  outliers start: 52
  outliers final: 36
  residues processed: 178
  average time/residue: 0.1700
  time to fit residues: 44.7034
Evaluate side-chains
  176 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 134
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  309 GLN
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  272 PHE
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  309 GLN
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  562 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 107 optimal weight:   20.0000
   chunk 106 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 102 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 537 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.203335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.149055 restraints weight = 11144.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.148208 restraints weight = 10758.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.150309 restraints weight = 8480.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9050  Z= 0.238
  Angle     :  0.630  10.080  12230  Z= 0.319
  Chirality :  0.041   0.137   1454
  Planarity :  0.004   0.057   1548
  Dihedral  :  3.907  21.287   1250
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  6.65 %
    Allowed  : 21.47 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.25), residues: 1146
  helix:  1.50 (0.19), residues: 746
  sheet:  0.23 (0.77), residues: 44
  loop : -1.18 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  66 
 HIS   0.007   0.001   HIS A 107 
 PHE   0.026   0.002   PHE A 429 
 TYR   0.020   0.001   TYR B 130 
 ARG   0.017   0.000   ARG B  61 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 144
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.8040 (t70) cc_final: 0.7596 (t70)
REVERT: A  203 VAL cc_start: 0.6390 (OUTLIER) cc_final: 0.6002 (t)
REVERT: A  210 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.5954 (ttm)
REVERT: A  216 GLU cc_start: 0.8562 (tp30) cc_final: 0.8309 (tp30)
REVERT: A  309 GLN cc_start: 0.6662 (OUTLIER) cc_final: 0.6179 (tt0)
REVERT: A  495 LEU cc_start: 0.8661 (mm) cc_final: 0.8416 (mm)
REVERT: B  125 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6044 (tp)
REVERT: B  250 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7440 (tp)
REVERT: B  309 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.6125 (tt0)
REVERT: B  332 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8226 (mmtt)
REVERT: B  395 ILE cc_start: 0.6365 (OUTLIER) cc_final: 0.5723 (tp)
REVERT: B  466 MET cc_start: 0.8610 (mmm) cc_final: 0.8072 (mmm)
REVERT: B  495 LEU cc_start: 0.8748 (mm) cc_final: 0.8456 (mm)
  outliers start: 65
  outliers final: 47
  residues processed: 188
  average time/residue: 0.1662
  time to fit residues: 46.1238
Evaluate side-chains
  185 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 130
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  309 GLN
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  272 PHE
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  309 GLN
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  332 LYS
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  562 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 111 optimal weight:    9.9990
   chunk 74 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4391 r_free = 0.4391 target = 0.204906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.150973 restraints weight = 11165.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.149967 restraints weight = 11531.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.152432 restraints weight = 9452.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9050  Z= 0.208
  Angle     :  0.616   9.232  12230  Z= 0.313
  Chirality :  0.041   0.136   1454
  Planarity :  0.004   0.040   1548
  Dihedral  :  3.836  21.284   1250
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 22.80 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.25), residues: 1146
  helix:  1.52 (0.19), residues: 748
  sheet:  0.30 (0.77), residues: 44
  loop : -1.12 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  66 
 HIS   0.005   0.001   HIS A 107 
 PHE   0.022   0.002   PHE A 429 
 TYR   0.010   0.001   TYR B 410 
 ARG   0.007   0.000   ARG A 190 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 133
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.7981 (t70) cc_final: 0.7557 (t70)
REVERT: A  203 VAL cc_start: 0.6070 (OUTLIER) cc_final: 0.5743 (t)
REVERT: A  210 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5809 (ttm)
REVERT: A  216 GLU cc_start: 0.8550 (tp30) cc_final: 0.8314 (tp30)
REVERT: A  309 GLN cc_start: 0.6598 (OUTLIER) cc_final: 0.6155 (tt0)
REVERT: A  495 LEU cc_start: 0.8679 (mm) cc_final: 0.8422 (mm)
REVERT: B  125 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6019 (tp)
REVERT: B  250 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7417 (tp)
REVERT: B  309 GLN cc_start: 0.6548 (OUTLIER) cc_final: 0.6131 (tt0)
REVERT: B  332 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8230 (mmtt)
REVERT: B  335 ILE cc_start: 0.8850 (tp) cc_final: 0.8612 (pt)
REVERT: B  395 ILE cc_start: 0.6259 (OUTLIER) cc_final: 0.5590 (tp)
REVERT: B  466 MET cc_start: 0.8599 (mmm) cc_final: 0.7990 (mmm)
  outliers start: 60
  outliers final: 43
  residues processed: 175
  average time/residue: 0.1736
  time to fit residues: 44.2665
Evaluate side-chains
  177 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 126
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  309 GLN
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  272 PHE
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  309 GLN
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  332 LYS
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  562 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 112 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 109 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 98 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 537 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.189187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.131498 restraints weight = 11237.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.131938 restraints weight = 8135.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.133057 restraints weight = 7412.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9050  Z= 0.300
  Angle     :  0.685  10.426  12230  Z= 0.349
  Chirality :  0.043   0.178   1454
  Planarity :  0.004   0.041   1548
  Dihedral  :  3.947  20.388   1250
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  7.26 %
    Allowed  : 21.78 %
    Favored  : 70.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.24), residues: 1146
  helix:  1.35 (0.19), residues: 746
  sheet:  0.36 (0.77), residues: 44
  loop : -1.07 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  66 
 HIS   0.007   0.001   HIS A 107 
 PHE   0.031   0.002   PHE B 429 
 TYR   0.019   0.002   TYR B 439 
 ARG   0.010   0.000   ARG A 190 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 132
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.8136 (t70) cc_final: 0.7611 (t70)
REVERT: A  216 GLU cc_start: 0.8764 (tp30) cc_final: 0.8448 (tp30)
REVERT: A  309 GLN cc_start: 0.6498 (OUTLIER) cc_final: 0.6239 (tt0)
REVERT: A  495 LEU cc_start: 0.8855 (mm) cc_final: 0.8521 (mm)
REVERT: B  125 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.5826 (tp)
REVERT: B  250 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7136 (tp)
REVERT: B  309 GLN cc_start: 0.6465 (OUTLIER) cc_final: 0.6213 (tt0)
REVERT: B  395 ILE cc_start: 0.6336 (OUTLIER) cc_final: 0.5820 (tp)
REVERT: B  466 MET cc_start: 0.8538 (mmm) cc_final: 0.7848 (mmm)
REVERT: B  495 LEU cc_start: 0.8928 (mm) cc_final: 0.8531 (mm)
  outliers start: 71
  outliers final: 52
  residues processed: 182
  average time/residue: 0.1689
  time to fit residues: 45.1105
Evaluate side-chains
  181 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 124
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  309 GLN
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  272 PHE
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  309 GLN
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  562 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 106 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 99 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 86 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 107 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   chunk 102 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4209 r_free = 0.4209 target = 0.192936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.135301 restraints weight = 11234.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.137844 restraints weight = 7650.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.138503 restraints weight = 6774.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7005
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9050  Z= 0.199
  Angle     :  0.640  11.410  12230  Z= 0.315
  Chirality :  0.041   0.175   1454
  Planarity :  0.004   0.039   1548
  Dihedral  :  3.839  22.348   1250
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 23.42 %
    Favored  : 71.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.25), residues: 1146
  helix:  1.46 (0.19), residues: 756
  sheet:  0.50 (0.81), residues: 44
  loop : -0.90 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  66 
 HIS   0.006   0.001   HIS A 107 
 PHE   0.023   0.002   PHE A 429 
 TYR   0.016   0.001   TYR B 439 
 ARG   0.009   0.000   ARG A 190 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 134
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.8064 (t70) cc_final: 0.7563 (t70)
REVERT: A  125 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5655 (tp)
REVERT: A  190 ARG cc_start: 0.8466 (mtm-85) cc_final: 0.8119 (mtm-85)
REVERT: A  216 GLU cc_start: 0.8673 (tp30) cc_final: 0.8391 (tp30)
REVERT: A  309 GLN cc_start: 0.6408 (OUTLIER) cc_final: 0.6130 (tt0)
REVERT: A  495 LEU cc_start: 0.8831 (mm) cc_final: 0.8501 (mm)
REVERT: B  125 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.5853 (tp)
REVERT: B  250 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7160 (tp)
REVERT: B  309 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.6046 (tt0)
REVERT: B  395 ILE cc_start: 0.6272 (OUTLIER) cc_final: 0.5717 (tp)
REVERT: B  466 MET cc_start: 0.8474 (mmm) cc_final: 0.7813 (mmm)
  outliers start: 52
  outliers final: 42
  residues processed: 174
  average time/residue: 0.1790
  time to fit residues: 45.1472
Evaluate side-chains
  175 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 127
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  309 GLN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  272 PHE
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  309 GLN
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  562 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 76 optimal weight:    8.9990
   chunk 28 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0070
   chunk 72 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 113 optimal weight:    8.9990
   chunk 44 optimal weight:    8.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
A 537 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.193506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.136126 restraints weight = 11102.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.138138 restraints weight = 7443.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.138927 restraints weight = 6409.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6995
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9050  Z= 0.188
  Angle     :  0.638  14.977  12230  Z= 0.313
  Chirality :  0.041   0.164   1454
  Planarity :  0.004   0.043   1548
  Dihedral  :  3.813  20.976   1250
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 23.82 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.25), residues: 1146
  helix:  1.56 (0.19), residues: 754
  sheet:  0.60 (0.82), residues: 44
  loop : -0.93 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  66 
 HIS   0.006   0.001   HIS A 107 
 PHE   0.021   0.002   PHE A  13 
 TYR   0.012   0.001   TYR B 410 
 ARG   0.007   0.000   ARG A 190 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 133
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.8033 (t70) cc_final: 0.7538 (t70)
REVERT: A  125 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5672 (tp)
REVERT: A  190 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.8168 (mtm-85)
REVERT: A  216 GLU cc_start: 0.8625 (tp30) cc_final: 0.8371 (tp30)
REVERT: A  309 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.6184 (tt0)
REVERT: B  125 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.5746 (tp)
REVERT: B  250 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7303 (tp)
REVERT: B  395 ILE cc_start: 0.6303 (OUTLIER) cc_final: 0.5755 (tp)
REVERT: B  466 MET cc_start: 0.8494 (mmm) cc_final: 0.7814 (mmm)
  outliers start: 50
  outliers final: 39
  residues processed: 170
  average time/residue: 0.2068
  time to fit residues: 50.6965
Evaluate side-chains
  172 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 128
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  309 GLN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  272 PHE
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  502 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 69 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 85 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9980
   chunk 113 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 326 GLN
B 537 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.193588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.128313 restraints weight = 11174.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.133798 restraints weight = 6146.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.137200 restraints weight = 4338.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.3247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9050  Z= 0.204
  Angle     :  0.644  14.634  12230  Z= 0.317
  Chirality :  0.041   0.160   1454
  Planarity :  0.004   0.064   1548
  Dihedral  :  3.852  22.286   1250
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 23.72 %
    Favored  : 71.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.25), residues: 1146
  helix:  1.54 (0.19), residues: 754
  sheet:  0.89 (0.86), residues: 44
  loop : -0.94 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  66 
 HIS   0.007   0.001   HIS A 107 
 PHE   0.018   0.002   PHE A 429 
 TYR   0.012   0.001   TYR B 410 
 ARG   0.006   0.000   ARG A 190 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 131
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.8083 (t70) cc_final: 0.7565 (t70)
REVERT: A  125 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.5809 (tp)
REVERT: A  190 ARG cc_start: 0.8468 (mtm-85) cc_final: 0.8113 (mtm-85)
REVERT: A  216 GLU cc_start: 0.8706 (tp30) cc_final: 0.8446 (tp30)
REVERT: A  309 GLN cc_start: 0.6365 (OUTLIER) cc_final: 0.6153 (tt0)
REVERT: A  465 LYS cc_start: 0.8921 (tttt) cc_final: 0.8238 (pttm)
REVERT: B  125 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.5866 (tp)
REVERT: B  250 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7201 (tp)
REVERT: B  466 MET cc_start: 0.8353 (mmm) cc_final: 0.7725 (mmm)
  outliers start: 50
  outliers final: 43
  residues processed: 173
  average time/residue: 0.1705
  time to fit residues: 42.8490
Evaluate side-chains
  172 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 125
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  309 GLN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain A residue  577 LYS
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  272 PHE
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  502 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 83 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   chunk 84 optimal weight:    0.8980
   chunk 92 optimal weight:   10.0000
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 537 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.192735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.127070 restraints weight = 11132.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.132562 restraints weight = 6096.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.135988 restraints weight = 4295.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9050  Z= 0.207
  Angle     :  0.661  14.445  12230  Z= 0.325
  Chirality :  0.042   0.156   1454
  Planarity :  0.004   0.068   1548
  Dihedral  :  3.867  20.559   1250
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 23.82 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.25), residues: 1146
  helix:  1.54 (0.19), residues: 754
  sheet:  2.71 (1.11), residues: 24
  loop : -1.01 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  66 
 HIS   0.007   0.001   HIS A 107 
 PHE   0.022   0.002   PHE A  13 
 TYR   0.015   0.001   TYR B 439 
 ARG   0.006   0.000   ARG A 190 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2982.04 seconds
wall clock time: 53 minutes 17.54 seconds (3197.54 seconds total)