Starting phenix.real_space_refine
on Sat Aug 23 01:12:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tss_41600/08_2025/8tss_41600.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tss_41600/08_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_41600/08_2025/8tss_41600.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tss_41600/08_2025/8tss_41600.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tss_41600/08_2025/8tss_41600.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tss_41600/08_2025/8tss_41600.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.35, per 1000 atoms: 0.26
  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: 0.92
  Conformation dependent library (CDL) restraints added in 325.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.31
  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: 1.45

  Time building geometry restraints manager: 1.17 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: 0.02
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:             1.270
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.760
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.810
-------------------------------------------------------------------------------
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= 0.187
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.014   0.001   ARG B 190 
 TYR   0.019   0.001   TYR B 439 
 PHE   0.026   0.002   PHE A 116 
 TRP   0.026   0.002   TRP A  66 
 HIS   0.015   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 9050)
  covalent geometry    : angle       0.75025 (12230)
  hydrogen bonds       : bond        0.16852 (  575)
  hydrogen bonds       : angle       6.08260 ( 1689)

*********************** 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  : 0.331 
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: 0.0999
  time to fit residues: 19.6527
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  : 0.351 
-------------------------------------------------------------------------------
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 108 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4231 r_free = 0.4231 target = 0.194574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.136835 restraints weight = 11001.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.138555 restraints weight = 6854.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.139698 restraints weight = 5675.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.140886 restraints weight = 4670.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.141583 restraints weight = 4501.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6904
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9050  Z= 0.156
  Angle     :  0.615   7.852  12230  Z= 0.320
  Chirality :  0.042   0.153   1454
  Planarity :  0.005   0.060   1548
  Dihedral  :  4.631  51.444   1257
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 20.25 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.25), residues: 1146
  helix:  1.39 (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
 ARG   0.007   0.001   ARG A 455 
 TYR   0.011   0.001   TYR B 439 
 PHE   0.016   0.002   PHE B 429 
 TRP   0.017   0.002   TRP B  66 
 HIS   0.015   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9050)
  covalent geometry    : angle       0.61451 (12230)
  hydrogen bonds       : bond        0.05993 (  575)
  hydrogen bonds       : angle       4.83467 ( 1689)

*********************** 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
  190 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 146
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.7970 (t70) cc_final: 0.7569 (t70)
REVERT: A  578 MET cc_start: 0.6153 (pmm) cc_final: 0.5908 (pmm)
REVERT: B  107 HIS cc_start: 0.8171 (t70) cc_final: 0.7783 (t70)
  outliers start: 44
  outliers final: 22
  residues processed: 175
  average time/residue: 0.0953
  time to fit residues: 23.4212
Evaluate side-chains
  152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
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   92 VAL
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 29 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0670
   chunk 11 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 33 optimal weight:    9.9990
   chunk 62 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 53 optimal weight:   10.0000
   chunk 101 optimal weight:    6.9990
   chunk 95 optimal weight:    0.8980
   overall best weight:    0.7120

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.195841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.137647 restraints weight = 11018.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.140263 restraints weight = 6826.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.141155 restraints weight = 5342.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.142458 restraints weight = 4521.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.142867 restraints weight = 4322.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6906
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9050  Z= 0.144
  Angle     :  0.602   7.705  12230  Z= 0.306
  Chirality :  0.041   0.157   1454
  Planarity :  0.004   0.053   1548
  Dihedral  :  3.792  18.772   1250
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 20.14 %
    Favored  : 74.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.25), residues: 1146
  helix:  1.48 (0.19), residues: 762
  sheet:  0.33 (0.79), residues: 44
  loop : -1.30 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 190 
 TYR   0.014   0.001   TYR A 439 
 PHE   0.019   0.002   PHE B 429 
 TRP   0.019   0.001   TRP B  66 
 HIS   0.008   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9050)
  covalent geometry    : angle       0.60240 (12230)
  hydrogen bonds       : bond        0.05570 (  575)
  hydrogen bonds       : angle       4.53501 ( 1689)

*********************** 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
  193 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 144
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.7947 (t70) cc_final: 0.7470 (t70)
REVERT: A  203 VAL cc_start: 0.6274 (OUTLIER) cc_final: 0.5928 (t)
REVERT: A  210 MET cc_start: 0.6173 (OUTLIER) cc_final: 0.5747 (ttm)
REVERT: A  242 MET cc_start: 0.6822 (mmt) cc_final: 0.6465 (mmt)
REVERT: A  318 LEU cc_start: 0.7162 (mt) cc_final: 0.6859 (tt)
REVERT: B  107 HIS cc_start: 0.8082 (t70) cc_final: 0.7638 (t70)
REVERT: B  537 HIS cc_start: 0.6262 (t-170) cc_final: 0.5980 (t-170)
REVERT: B  578 MET cc_start: 0.5208 (pmm) cc_final: 0.4907 (pmm)
  outliers start: 49
  outliers final: 31
  residues processed: 176
  average time/residue: 0.0902
  time to fit residues: 22.7595
Evaluate side-chains
  164 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
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   92 VAL
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  320 THR
Chi-restraints excluded: chain A residue  375 VAL
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  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  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  320 THR
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  463 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 51 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 27 optimal weight:    0.3980
   chunk 39 optimal weight:    8.9990
   chunk 60 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 214 HIS
B 195 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.192356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.127607 restraints weight = 11416.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.133249 restraints weight = 6217.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.136775 restraints weight = 4400.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.138743 restraints weight = 3627.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.139692 restraints weight = 3257.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9050  Z= 0.158
  Angle     :  0.614   7.759  12230  Z= 0.314
  Chirality :  0.041   0.133   1454
  Planarity :  0.004   0.045   1548
  Dihedral  :  3.810  19.790   1250
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 20.65 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.25), residues: 1146
  helix:  1.54 (0.19), residues: 746
  sheet:  0.27 (0.78), residues: 44
  loop : -1.17 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 354 
 TYR   0.021   0.002   TYR A 268 
 PHE   0.024   0.002   PHE A 429 
 TRP   0.020   0.002   TRP B  66 
 HIS   0.010   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 9050)
  covalent geometry    : angle       0.61392 (12230)
  hydrogen bonds       : bond        0.05606 (  575)
  hydrogen bonds       : angle       4.51675 ( 1689)

*********************** 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
  196 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 137
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7817 (mm)
REVERT: A  107 HIS cc_start: 0.7996 (t70) cc_final: 0.7517 (t70)
REVERT: A  203 VAL cc_start: 0.6234 (OUTLIER) cc_final: 0.5906 (t)
REVERT: A  210 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5731 (ttm)
REVERT: A  216 GLU cc_start: 0.8674 (tp30) cc_final: 0.8293 (tp30)
REVERT: A  309 GLN cc_start: 0.6431 (OUTLIER) cc_final: 0.5958 (tt0)
REVERT: B  107 HIS cc_start: 0.8125 (t70) cc_final: 0.7702 (t70)
REVERT: B  309 GLN cc_start: 0.6385 (OUTLIER) cc_final: 0.5941 (tt0)
REVERT: B  395 ILE cc_start: 0.6425 (OUTLIER) cc_final: 0.5712 (tp)
REVERT: B  466 MET cc_start: 0.8422 (mmm) cc_final: 0.7758 (mmm)
REVERT: B  495 LEU cc_start: 0.8855 (mm) cc_final: 0.8451 (mm)
REVERT: B  537 HIS cc_start: 0.6815 (t-170) cc_final: 0.6439 (t-90)
REVERT: B  578 MET cc_start: 0.5332 (pmm) cc_final: 0.5119 (pmm)
  outliers start: 59
  outliers final: 38
  residues processed: 181
  average time/residue: 0.0773
  time to fit residues: 20.5057
Evaluate side-chains
  174 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 130
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   64 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  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  375 VAL
Chi-restraints excluded: chain A residue  389 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 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  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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 58 optimal weight:    0.4980
   chunk 82 optimal weight:    0.5980
   chunk 39 optimal weight:   10.0000
   chunk 78 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 91 optimal weight:    0.8980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.4224 r_free = 0.4224 target = 0.194915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.136494 restraints weight = 11202.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.138434 restraints weight = 7370.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.139558 restraints weight = 6390.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.140135 restraints weight = 4749.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.140568 restraints weight = 4506.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
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      :  0.003   0.032   9050  Z= 0.139
  Angle     :  0.593  10.092  12230  Z= 0.300
  Chirality :  0.040   0.129   1454
  Planarity :  0.004   0.074   1548
  Dihedral  :  3.811  22.267   1250
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 22.09 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.25), residues: 1146
  helix:  1.62 (0.19), residues: 748
  sheet:  0.17 (0.76), residues: 44
  loop : -1.10 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B  61 
 TYR   0.021   0.001   TYR A 268 
 PHE   0.022   0.002   PHE A 429 
 TRP   0.018   0.001   TRP B  66 
 HIS   0.005   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9050)
  covalent geometry    : angle       0.59316 (12230)
  hydrogen bonds       : bond        0.05293 (  575)
  hydrogen bonds       : angle       4.34296 ( 1689)

*********************** 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
  190 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 139
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.7977 (t70) cc_final: 0.7432 (t70)
REVERT: A  203 VAL cc_start: 0.6118 (OUTLIER) cc_final: 0.5788 (t)
REVERT: A  210 MET cc_start: 0.6293 (OUTLIER) cc_final: 0.5913 (ttm)
REVERT: A  216 GLU cc_start: 0.8695 (tp30) cc_final: 0.8399 (tp30)
REVERT: A  309 GLN cc_start: 0.6356 (OUTLIER) cc_final: 0.5941 (tt0)
REVERT: A  495 LEU cc_start: 0.8805 (mm) cc_final: 0.8495 (mm)
REVERT: B  107 HIS cc_start: 0.8148 (t70) cc_final: 0.7750 (t70)
REVERT: B  125 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.5758 (tp)
REVERT: B  309 GLN cc_start: 0.6341 (OUTLIER) cc_final: 0.5950 (tt0)
REVERT: B  395 ILE cc_start: 0.6467 (OUTLIER) cc_final: 0.5743 (tp)
REVERT: B  435 ASN cc_start: 0.5506 (m-40) cc_final: 0.5127 (t0)
REVERT: B  466 MET cc_start: 0.8505 (mmm) cc_final: 0.7770 (mmm)
REVERT: B  495 LEU cc_start: 0.8838 (mm) cc_final: 0.8494 (mm)
REVERT: B  537 HIS cc_start: 0.6392 (t-170) cc_final: 0.6134 (t-90)
REVERT: B  578 MET cc_start: 0.5489 (pmm) cc_final: 0.5216 (pmm)
  outliers start: 51
  outliers final: 36
  residues processed: 177
  average time/residue: 0.0809
  time to fit residues: 20.8907
Evaluate side-chains
  173 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 131
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   85 SER
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  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  375 VAL
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  577 LYS
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  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  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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 47 optimal weight:    0.4980
   chunk 6 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0980
   chunk 0 optimal weight:    8.9990
   chunk 41 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4237 r_free = 0.4237 target = 0.196543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.138458 restraints weight = 11173.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.139826 restraints weight = 7218.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.140984 restraints weight = 6646.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.141781 restraints weight = 4732.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.142224 restraints weight = 4478.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9050  Z= 0.132
  Angle     :  0.600  10.448  12230  Z= 0.303
  Chirality :  0.041   0.148   1454
  Planarity :  0.004   0.040   1548
  Dihedral  :  3.781  22.582   1250
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 21.98 %
    Favored  : 72.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.25), residues: 1146
  helix:  1.57 (0.19), residues: 764
  sheet:  0.27 (0.77), residues: 44
  loop : -1.11 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 190 
 TYR   0.022   0.001   TYR A 268 
 PHE   0.022   0.002   PHE B 429 
 TRP   0.020   0.001   TRP A  66 
 HIS   0.006   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9050)
  covalent geometry    : angle       0.60046 (12230)
  hydrogen bonds       : bond        0.05118 (  575)
  hydrogen bonds       : angle       4.27603 ( 1689)

*********************** 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
  183 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 132
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.7926 (t70) cc_final: 0.7382 (t70)
REVERT: A  190 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8177 (mtm-85)
REVERT: A  203 VAL cc_start: 0.5646 (OUTLIER) cc_final: 0.5355 (t)
REVERT: A  210 MET cc_start: 0.6285 (OUTLIER) cc_final: 0.5882 (ttm)
REVERT: A  216 GLU cc_start: 0.8613 (tp30) cc_final: 0.8288 (tp30)
REVERT: A  309 GLN cc_start: 0.6392 (OUTLIER) cc_final: 0.6021 (tt0)
REVERT: A  495 LEU cc_start: 0.8834 (mm) cc_final: 0.8506 (mm)
REVERT: B  107 HIS cc_start: 0.8003 (t70) cc_final: 0.7614 (t70)
REVERT: B  125 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.5833 (tp)
REVERT: B  332 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8269 (mmtt)
REVERT: B  395 ILE cc_start: 0.6479 (OUTLIER) cc_final: 0.5720 (tp)
REVERT: B  466 MET cc_start: 0.8447 (mmm) cc_final: 0.7735 (mmm)
REVERT: B  537 HIS cc_start: 0.6399 (t-170) cc_final: 0.6123 (t-90)
REVERT: B  578 MET cc_start: 0.5585 (pmm) cc_final: 0.5260 (pmm)
  outliers start: 51
  outliers final: 38
  residues processed: 170
  average time/residue: 0.0839
  time to fit residues: 20.2368
Evaluate side-chains
  168 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 124
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
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   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  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  312 MET
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  501 ILE
Chi-restraints excluded: chain A residue  577 LYS
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  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  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 96 optimal weight:   10.0000
   chunk 15 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 113 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 106 optimal weight:    2.9990
   chunk 111 optimal weight:    6.9990
   chunk 11 optimal weight:    0.2980
   chunk 41 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.4199 r_free = 0.4199 target = 0.192264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.125412 restraints weight = 11269.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.131088 restraints weight = 6061.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.134716 restraints weight = 4237.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.136861 restraints weight = 3456.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.137944 restraints weight = 3085.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
moved from start:          0.2855

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= 0.160
  Angle     :  0.624   9.801  12230  Z= 0.318
  Chirality :  0.041   0.141   1454
  Planarity :  0.004   0.039   1548
  Dihedral  :  3.799  20.072   1250
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 21.27 %
    Favored  : 72.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.25), residues: 1146
  helix:  1.62 (0.19), residues: 746
  sheet:  0.34 (0.77), residues: 44
  loop : -1.04 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 354 
 TYR   0.023   0.001   TYR A 268 
 PHE   0.026   0.002   PHE B 429 
 TRP   0.022   0.002   TRP A  66 
 HIS   0.007   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9050)
  covalent geometry    : angle       0.62360 (12230)
  hydrogen bonds       : bond        0.05534 (  575)
  hydrogen bonds       : angle       4.40566 ( 1689)

*********************** 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
  191 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 131
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.8021 (t70) cc_final: 0.7522 (t70)
REVERT: A  203 VAL cc_start: 0.5644 (OUTLIER) cc_final: 0.5328 (t)
REVERT: A  210 MET cc_start: 0.6175 (OUTLIER) cc_final: 0.5750 (ttm)
REVERT: A  216 GLU cc_start: 0.8728 (tp30) cc_final: 0.8395 (tp30)
REVERT: A  309 GLN cc_start: 0.6379 (OUTLIER) cc_final: 0.6118 (tt0)
REVERT: A  495 LEU cc_start: 0.8932 (mm) cc_final: 0.8563 (mm)
REVERT: B  125 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6028 (tp)
REVERT: B  309 GLN cc_start: 0.6338 (OUTLIER) cc_final: 0.6002 (tt0)
REVERT: B  332 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8263 (mmtt)
REVERT: B  395 ILE cc_start: 0.6393 (OUTLIER) cc_final: 0.5556 (tp)
REVERT: B  466 MET cc_start: 0.8349 (mmm) cc_final: 0.7682 (mmm)
REVERT: B  537 HIS cc_start: 0.6759 (t-170) cc_final: 0.6316 (t-90)
REVERT: B  578 MET cc_start: 0.5835 (pmm) cc_final: 0.5618 (pmm)
  outliers start: 60
  outliers final: 45
  residues processed: 175
  average time/residue: 0.0862
  time to fit residues: 21.6232
Evaluate side-chains
  178 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 126
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
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   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  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  324 SER
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  501 ILE
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain A residue  577 LYS
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  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  321 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0970
   chunk 18 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 27 optimal weight:    0.3980
   chunk 74 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 6 optimal weight:    0.4980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.4222 r_free = 0.4222 target = 0.195293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.137362 restraints weight = 11180.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.138000 restraints weight = 7585.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.138663 restraints weight = 6799.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.139744 restraints weight = 5297.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.140163 restraints weight = 4934.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9050  Z= 0.134
  Angle     :  0.605   9.686  12230  Z= 0.303
  Chirality :  0.041   0.186   1454
  Planarity :  0.004   0.051   1548
  Dihedral  :  3.745  19.186   1250
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 23.21 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.25), residues: 1146
  helix:  1.67 (0.19), residues: 750
  sheet:  0.24 (0.71), residues: 56
  loop : -0.96 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 190 
 TYR   0.023   0.001   TYR A 268 
 PHE   0.024   0.002   PHE B 429 
 TRP   0.019   0.001   TRP B  66 
 HIS   0.006   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 9050)
  covalent geometry    : angle       0.60479 (12230)
  hydrogen bonds       : bond        0.05128 (  575)
  hydrogen bonds       : angle       4.26953 ( 1689)

*********************** 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
  177 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 130
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.7968 (t70) cc_final: 0.7418 (t70)
REVERT: A  203 VAL cc_start: 0.5413 (OUTLIER) cc_final: 0.5169 (t)
REVERT: A  210 MET cc_start: 0.6029 (OUTLIER) cc_final: 0.5637 (ttm)
REVERT: A  216 GLU cc_start: 0.8613 (tp30) cc_final: 0.8335 (tp30)
REVERT: A  309 GLN cc_start: 0.6393 (OUTLIER) cc_final: 0.6153 (tt0)
REVERT: B  125 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.5793 (tp)
REVERT: B  309 GLN cc_start: 0.6366 (OUTLIER) cc_final: 0.6052 (tt0)
REVERT: B  332 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8282 (mmtt)
REVERT: B  395 ILE cc_start: 0.6361 (OUTLIER) cc_final: 0.5605 (tp)
REVERT: B  466 MET cc_start: 0.8436 (mmm) cc_final: 0.7797 (mmm)
REVERT: B  537 HIS cc_start: 0.6429 (t-170) cc_final: 0.6114 (t-90)
  outliers start: 47
  outliers final: 38
  residues processed: 165
  average time/residue: 0.0832
  time to fit residues: 19.6155
Evaluate side-chains
  173 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 128
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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  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  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  501 ILE
Chi-restraints excluded: chain A residue  577 LYS
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  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  321 ILE
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  495 LEU
Chi-restraints excluded: chain B residue  502 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 36 optimal weight:    8.9990
   chunk 55 optimal weight:   10.0000
   chunk 106 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 96 optimal weight:    7.9990
   chunk 113 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.3188

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.197600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.144592 restraints weight = 11503.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.141324 restraints weight = 12643.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.143748 restraints weight = 11299.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.144077 restraints weight = 7654.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.144524 restraints weight = 7534.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   9050  Z= 0.273
  Angle     :  0.758   9.660  12230  Z= 0.392
  Chirality :  0.045   0.174   1454
  Planarity :  0.004   0.041   1548
  Dihedral  :  4.088  21.238   1250
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  6.54 %
    Allowed  : 21.47 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.24), residues: 1146
  helix:  1.21 (0.19), residues: 744
  sheet:  0.43 (0.71), residues: 54
  loop : -1.12 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 190 
 TYR   0.027   0.002   TYR A 268 
 PHE   0.039   0.003   PHE B 429 
 TRP   0.029   0.002   TRP B  66 
 HIS   0.008   0.002   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00648 ( 9050)
  covalent geometry    : angle       0.75842 (12230)
  hydrogen bonds       : bond        0.06561 (  575)
  hydrogen bonds       : angle       4.81098 ( 1689)

*********************** 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
  193 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 129
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6238 (tp)
REVERT: A  216 GLU cc_start: 0.8652 (tp30) cc_final: 0.8356 (tp30)
REVERT: A  249 SER cc_start: 0.7616 (t) cc_final: 0.7403 (t)
REVERT: A  309 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6511 (tt0)
REVERT: A  429 PHE cc_start: 0.6200 (p90) cc_final: 0.5613 (p90)
REVERT: A  465 LYS cc_start: 0.8981 (tttt) cc_final: 0.8323 (pttm)
REVERT: A  495 LEU cc_start: 0.8739 (mm) cc_final: 0.8428 (mm)
REVERT: B  125 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6229 (tp)
REVERT: B  309 GLN cc_start: 0.6733 (OUTLIER) cc_final: 0.6491 (tt0)
REVERT: B  395 ILE cc_start: 0.6302 (OUTLIER) cc_final: 0.5916 (tp)
REVERT: B  429 PHE cc_start: 0.6273 (p90) cc_final: 0.5757 (p90)
REVERT: B  466 MET cc_start: 0.8560 (mmm) cc_final: 0.7992 (mmm)
  outliers start: 64
  outliers final: 46
  residues processed: 177
  average time/residue: 0.0813
  time to fit residues: 21.2663
Evaluate side-chains
  171 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 120
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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   92 VAL
Chi-restraints excluded: chain A residue   96 VAL
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  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  324 SER
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  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   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  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  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  395 ILE
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  562 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 39 optimal weight:    8.9990
   chunk 29 optimal weight:    0.7980
   chunk 96 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4191 r_free = 0.4191 target = 0.191526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.125674 restraints weight = 11126.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.131070 restraints weight = 6087.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.134393 restraints weight = 4300.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.136402 restraints weight = 3545.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.137694 restraints weight = 3169.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6992
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9050  Z= 0.156
  Angle     :  0.658  10.084  12230  Z= 0.329
  Chirality :  0.042   0.181   1454
  Planarity :  0.004   0.053   1548
  Dihedral  :  3.956  22.513   1250
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 23.72 %
    Favored  : 72.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.25), residues: 1146
  helix:  1.44 (0.19), residues: 746
  sheet:  1.83 (0.95), residues: 34
  loop : -1.25 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 190 
 TYR   0.024   0.001   TYR A 268 
 PHE   0.024   0.002   PHE B 429 
 TRP   0.018   0.002   TRP B  66 
 HIS   0.007   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9050)
  covalent geometry    : angle       0.65800 (12230)
  hydrogen bonds       : bond        0.05658 (  575)
  hydrogen bonds       : angle       4.43515 ( 1689)

********************** 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
  169 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 129
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.8088 (t70) cc_final: 0.7559 (t70)
REVERT: A  216 GLU cc_start: 0.8794 (tp30) cc_final: 0.8511 (tp30)
REVERT: A  309 GLN cc_start: 0.6355 (OUTLIER) cc_final: 0.6026 (tt0)
REVERT: A  465 LYS cc_start: 0.8941 (tttt) cc_final: 0.8277 (pttp)
REVERT: A  553 ASP cc_start: 0.7678 (t0) cc_final: 0.7449 (t0)
REVERT: B  125 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.5947 (tp)
REVERT: B  309 GLN cc_start: 0.6345 (OUTLIER) cc_final: 0.6010 (tt0)
REVERT: B  395 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.5722 (tp)
REVERT: B  429 PHE cc_start: 0.5877 (p90) cc_final: 0.5243 (p90)
REVERT: B  466 MET cc_start: 0.8332 (mmm) cc_final: 0.7681 (mmm)
  outliers start: 40
  outliers final: 36
  residues processed: 159
  average time/residue: 0.0888
  time to fit residues: 20.1787
Evaluate side-chains
  167 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 127
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
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   92 VAL
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  272 PHE
Chi-restraints excluded: chain A residue  295 MET
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  321 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  426 VAL
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   76 ILE
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  167 LEU
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  245 VAL
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  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  495 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 72 optimal weight:    0.5980
   chunk 109 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 17 optimal weight:    0.6980
   chunk 113 optimal weight:    8.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4209 r_free = 0.4209 target = 0.193693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.136395 restraints weight = 11045.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.138061 restraints weight = 7373.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.138618 restraints weight = 6779.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.139720 restraints weight = 5161.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.140056 restraints weight = 4718.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
moved from start:          0.3396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9050  Z= 0.142
  Angle     :  0.629   9.592  12230  Z= 0.315
  Chirality :  0.041   0.183   1454
  Planarity :  0.004   0.049   1548
  Dihedral  :  3.886  23.156   1250
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 23.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.25), residues: 1146
  helix:  1.52 (0.19), residues: 750
  sheet:  2.46 (1.12), residues: 24
  loop : -1.05 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 190 
 TYR   0.024   0.001   TYR A 268 
 PHE   0.021   0.002   PHE A  13 
 TRP   0.018   0.001   TRP B  66 
 HIS   0.007   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9050)
  covalent geometry    : angle       0.62900 (12230)
  hydrogen bonds       : bond        0.05178 (  575)
  hydrogen bonds       : angle       4.32306 ( 1689)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1549.97 seconds
wall clock time: 27 minutes 31.72 seconds (1651.72 seconds total)