Starting phenix.real_space_refine
on Thu Mar 13 13:00:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dmo_27545/03_2025/8dmo_27545.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dmo_27545/03_2025/8dmo_27545.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dmo_27545/03_2025/8dmo_27545.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dmo_27545/03_2025/8dmo_27545.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dmo_27545/03_2025/8dmo_27545.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dmo_27545/03_2025/8dmo_27545.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.015
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    5649      2.51       5
     N    1549      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 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8912
  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: 4453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 575, 4453
          Classifications: {'peptide': 575}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 561}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 5.77, per 1000 atoms: 0.65
  Number of scatterers: 8912
  At special positions: 0
  Unit cell: (89.46, 136.32, 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    1549      7.00
     C    5649      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.21
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 4 sheets defined
      71.2% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  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 47
      removed outlier: 3.570A  pdb=" N   LEU A  27 " --> pdb=" O   PHE A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 54
      removed outlier: 3.580A  pdb=" N   LEU A  51 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 109
      Proline residue:  A  68  - end of helix
    Processing helix  chain 'A' and resid 112 through 119
      removed outlier: 4.278A  pdb=" N   PHE A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 125
      removed outlier: 3.773A  pdb=" N   LEU A 125 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 128
      No H-bonds generated for 'chain 'A' and resid 126 through 128'
    Processing helix  chain 'A' and resid 130 through 164
    Processing helix  chain 'A' and resid 164 through 212
      Proline residue:  A 176  - end of helix
      removed outlier: 4.233A  pdb=" N   GLN A 202 " --> pdb=" O   ASN A 198 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   VAL A 203 " --> pdb=" O   THR A 199 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   SER A 206 " --> pdb=" O   GLN A 202 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ALA A 207 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   GLU A 208 " --> pdb=" O   THR A 204 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLN A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   MET A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LYS A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 221
      removed outlier: 3.748A  pdb=" N   ILE A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   PHE A 220 " --> pdb=" O   GLU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 272
      removed outlier: 4.441A  pdb=" N   ASP A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      removed outlier: 3.836A  pdb=" N   PHE A 272 " --> pdb=" O   TYR A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 277
      removed outlier: 3.818A  pdb=" N   ASP A 277 " --> pdb=" O   PRO A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 302
      removed outlier: 4.537A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 3.563A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 323
      removed outlier: 3.585A  pdb=" N   GLN A 307 " --> pdb=" O   ASN A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 390
      removed outlier: 3.928A  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: 4.090A  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
      removed outlier: 3.545A  pdb=" N   ASN A 464 " --> pdb=" O   MET A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 472
      removed outlier: 3.532A  pdb=" N   ASP A 471 " --> pdb=" O   ASN A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 497
      removed outlier: 3.618A  pdb=" N   ARG A 497 " --> pdb=" O   ARG A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 527
      removed outlier: 3.973A  pdb=" N   ILE A 519 " --> pdb=" O   SER A 515 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLN A 527 " --> pdb=" O   LEU A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 561 through 569
    Processing helix  chain 'A' and resid 570 through 578
    Processing helix  chain 'B' and resid 8 through 21
      removed outlier: 3.649A  pdb=" N   THR B  12 " --> pdb=" O   SER B   8 " (cutoff:3.500A)
      Proline residue:  B  18  - end of helix
    Processing helix  chain 'B' and resid 23 through 47
      removed outlier: 3.599A  pdb=" N   LEU B  27 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 54
      removed outlier: 3.681A  pdb=" N   LEU B  51 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 109
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 113 through 119
      removed outlier: 3.545A  pdb=" N   GLN B 119 " --> pdb=" O   PHE B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 130
      removed outlier: 3.756A  pdb=" N   ILE B 128 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 200
      removed outlier: 8.040A  pdb=" N   GLN B 166 " --> pdb=" O   TYR B 162 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   LEU B 167 " --> pdb=" O   TYR B 163 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   VAL B 173 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   LEU B 174 " --> pdb=" O   ILE B 170 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ALA B 175 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
      Proline residue:  B 176  - end of helix
    Processing helix  chain 'B' and resid 200 through 212
      removed outlier: 4.056A  pdb=" N   THR B 204 " --> pdb=" O   MET B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
      removed outlier: 5.161A  pdb=" N   ILE B 219 " --> pdb=" O   LYS B 215 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   PHE B 220 " --> pdb=" O   GLU B 216 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY B 221 " --> pdb=" O   VAL B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 250
      removed outlier: 3.598A  pdb=" N   GLN B 240 " --> pdb=" O   ARG B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 270
      removed outlier: 3.641A  pdb=" N   ILE B 254 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 277
      removed outlier: 3.811A  pdb=" N   ASP B 277 " --> pdb=" O   PRO B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 302
      removed outlier: 3.725A  pdb=" N   ILE B 284 " --> pdb=" O   THR B 280 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   THR B 285 " --> pdb=" O   ALA B 281 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   SER B 289 " --> pdb=" O   THR B 285 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   ARG B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
    Processing helix  chain 'B' and resid 303 through 323
      removed outlier: 3.618A  pdb=" N   GLN B 307 " --> pdb=" O   ASN B 303 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ILE B 321 " --> pdb=" O   THR B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 390
      removed outlier: 3.724A  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: 3.869A  pdb=" N   ALA B 438 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 445
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 459 through 464
    Processing helix  chain 'B' and resid 468 through 472
      removed outlier: 3.631A  pdb=" N   ASP B 471 " --> pdb=" O   ASN B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 497
    Processing helix  chain 'B' and resid 515 through 527
      removed outlier: 3.818A  pdb=" N   ILE B 519 " --> pdb=" O   SER B 515 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN B 527 " --> pdb=" O   LEU B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 542
    Processing helix  chain 'B' and resid 561 through 569
    Processing helix  chain 'B' and resid 570 through 578
    Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 366
      removed outlier: 6.401A  pdb=" N   ARG A 360 " --> pdb=" O   THR A 348 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   THR A 348 " --> pdb=" O   ARG A 360 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   ILE A 362 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
      removed outlier: 5.614A  pdb=" N   PHE A 344 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   LEU A 401 " --> pdb=" O   PHE A 344 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   ASN A 346 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      removed outlier: 4.780A  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 422
      removed outlier: 6.239A  pdb=" N   ALA A 420 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   VAL A 372 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   THR A 371 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   VAL A 549 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   VAL A 551 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   VAL A 375 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   GLU A 552 " --> pdb=" O   ILE A 556 " (cutoff:3.500A)
      removed outlier: 5.108A  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 366
      removed outlier: 6.548A  pdb=" N   ARG B 360 " --> pdb=" O   THR B 348 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   THR B 348 " --> pdb=" O   ARG B 360 " (cutoff:3.500A)
      removed outlier: 5.291A  pdb=" N   ILE B 362 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   PHE B 344 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   LEU B 401 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   ASN B 346 " --> pdb=" O   GLU B 399 " (cutoff:3.500A)
      removed outlier: 4.824A  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 422
      removed outlier: 6.544A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   THR B 371 " --> pdb=" O   GLU B 547 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   VAL B 549 " --> pdb=" O   THR B 371 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   VAL B 551 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   VAL B 375 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   ILE B 548 " --> pdb=" O   ARG B 559 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ARG B 559 " --> pdb=" O   ILE B 548 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL B 550 " --> pdb=" O   VAL B 557 " (cutoff:3.500A)

    574 hydrogen bonds defined for protein.
    1677 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.60

  Time building geometry restraints manager: 2.61 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2951
        1.34 -     1.46: 1909
        1.46 -     1.58: 4080
        1.58 -     1.70: 0
        1.70 -     1.82: 104
  Bond restraints: 9044
  Sorted by residual:
  bond pdb=" N   ILE B 172 "
       pdb=" CA  ILE B 172 "
    ideal  model  delta    sigma   weight residual
    1.459  1.440  0.019 1.25e-02 6.40e+03 2.37e+00
  bond pdb=" C   VAL A 356 "
       pdb=" N   PRO A 357 "
    ideal  model  delta    sigma   weight residual
    1.330  1.346 -0.015 1.19e-02 7.06e+03 1.66e+00
  bond pdb=" CB  PRO A 297 "
       pdb=" CG  PRO A 297 "
    ideal  model  delta    sigma   weight residual
    1.492  1.446  0.046 5.00e-02 4.00e+02 8.34e-01
  bond pdb=" CB  GLU B 336 "
       pdb=" CG  GLU B 336 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.36e-01
  bond pdb=" N   VAL B 173 "
       pdb=" CA  VAL B 173 "
    ideal  model  delta    sigma   weight residual
    1.459  1.470 -0.011 1.25e-02 6.40e+03 7.11e-01
  ... (remaining 9039 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 11996
        1.88 -     3.76: 181
        3.76 -     5.64: 35
        5.64 -     7.52: 6
        7.52 -     9.40: 5
  Bond angle restraints: 12223
  Sorted by residual:
  angle pdb=" C   ILE B 172 "
        pdb=" N   VAL B 173 "
        pdb=" CA  VAL B 173 "
      ideal   model   delta    sigma   weight residual
     121.97  127.75   -5.78 1.80e+00 3.09e-01 1.03e+01
  angle pdb=" CB  MET B 111 "
        pdb=" CG  MET B 111 "
        pdb=" SD  MET B 111 "
      ideal   model   delta    sigma   weight residual
     112.70  103.30    9.40 3.00e+00 1.11e-01 9.81e+00
  angle pdb=" CA  MET B 466 "
        pdb=" CB  MET B 466 "
        pdb=" CG  MET B 466 "
      ideal   model   delta    sigma   weight residual
     114.10  120.27   -6.17 2.00e+00 2.50e-01 9.51e+00
  angle pdb=" CB  MET B 196 "
        pdb=" CG  MET B 196 "
        pdb=" SD  MET B 196 "
      ideal   model   delta    sigma   weight residual
     112.70  121.56   -8.86 3.00e+00 1.11e-01 8.71e+00
  angle pdb=" CA  MET A 466 "
        pdb=" CB  MET A 466 "
        pdb=" CG  MET A 466 "
      ideal   model   delta    sigma   weight residual
     114.10  120.00   -5.90 2.00e+00 2.50e-01 8.70e+00
  ... (remaining 12218 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 4942
       17.92 -    35.85: 458
       35.85 -    53.77: 72
       53.77 -    71.70: 17
       71.70 -    89.62: 10
  Dihedral angle restraints: 5499
    sinusoidal: 2177
      harmonic: 3322
  Sorted by residual:
  dihedral pdb=" CA  MET B 111 "
           pdb=" C   MET B 111 "
           pdb=" N   PRO B 112 "
           pdb=" CA  PRO B 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.69  -26.31     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  MET A 466 "
           pdb=" C   MET A 466 "
           pdb=" N   ASP A 467 "
           pdb=" CA  ASP A 467 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.59  -18.41     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  MET B 466 "
           pdb=" C   MET B 466 "
           pdb=" N   ASP B 467 "
           pdb=" CA  ASP B 467 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.63  -18.37     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 5496 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 921
       0.033 -    0.066: 361
       0.066 -    0.099: 119
       0.099 -    0.132: 49
       0.132 -    0.165: 4
  Chirality restraints: 1454
  Sorted by residual:
  chirality pdb=" CB  ILE A 501 "
            pdb=" CA  ILE A 501 "
            pdb=" CG1 ILE A 501 "
            pdb=" CG2 ILE A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 6.82e-01
  chirality pdb=" CA  TRP B  17 "
            pdb=" N   TRP B  17 "
            pdb=" C   TRP B  17 "
            pdb=" CB  TRP B  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.17e-01
  chirality pdb=" CA  MET A 109 "
            pdb=" N   MET A 109 "
            pdb=" C   MET A 109 "
            pdb=" CB  MET A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.32e-01
  ... (remaining 1451 not shown)

  Planarity restraints: 1547
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 296 "   -0.028 5.00e-02 4.00e+02   4.24e-02 2.87e+00
        pdb=" N   PRO A 297 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 297 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 297 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 296 "    0.025 5.00e-02 4.00e+02   3.72e-02 2.21e+00
        pdb=" N   PRO B 297 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 297 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 297 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 252 "   -0.024 5.00e-02 4.00e+02   3.68e-02 2.17e+00
        pdb=" N   PRO A 253 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 253 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 253 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1544 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1636
        2.77 -     3.30: 9524
        3.30 -     3.84: 14652
        3.84 -     4.37: 15871
        4.37 -     4.90: 27705
  Nonbonded interactions: 69388
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  46 "
            pdb=" OH  TYR B 163 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OG1 THR B  12 "
            pdb=" OE1 GLN B 316 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OH  TYR B 351 "
            pdb=" OG1 THR B 384 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   THR A 280 "
            pdb=" OG1 THR A 283 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ASN B 363 "
            pdb=" NH2 ARG B 559 "
     model   vdw
     2.267 3.120
  ... (remaining 69383 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 7 through 496 or (resid 497 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 498 through 581))
  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:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     23.700
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9044  Z= 0.204
  Angle     :  0.626   9.395  12223  Z= 0.324
  Chirality :  0.042   0.165   1454
  Planarity :  0.004   0.042   1547
  Dihedral  : 14.363  89.619   3351
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.97 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.25), residues: 1146
  helix:  2.06 (0.20), residues: 682
  sheet:  1.07 (0.61), residues: 76
  loop : -0.37 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  10 
 HIS   0.005   0.001   HIS A 214 
 PHE   0.017   0.002   PHE B 115 
 TYR   0.015   0.001   TYR B 439 
 ARG   0.004   0.000   ARG A 102 

*********************** 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
  102 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.2348
  time to fit residues: 32.7586
Evaluate side-chains
  67 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 86 optimal weight:    3.9990
   chunk 47 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0370
   chunk 58 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   chunk 89 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 54 optimal weight:   10.0000
   chunk 66 optimal weight:    0.8980
   chunk 103 optimal weight:    4.9990
   overall best weight:    2.1864

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

Flipped N/Q/H residues before XYZ refinement:
A 223 GLN
A 326 GLN
A 436 ASN
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 GLN
B 316 GLN
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 520 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.034979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.025379 restraints weight = 81422.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.026180 restraints weight = 49944.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.026745 restraints weight = 36663.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8769
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9044  Z= 0.237
  Angle     :  0.627   9.520  12223  Z= 0.324
  Chirality :  0.042   0.141   1454
  Planarity :  0.004   0.042   1547
  Dihedral  :  3.961  18.895   1249
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.23 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 10.64 %
    Favored  : 88.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.25), residues: 1146
  helix:  1.97 (0.19), residues: 728
  sheet:  1.55 (0.59), residues: 70
  loop : -0.42 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  10 
 HIS   0.006   0.001   HIS A 427 
 PHE   0.014   0.002   PHE A 429 
 TYR   0.011   0.001   TYR B 439 
 ARG   0.005   0.001   ARG A 190 

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

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9475 (tpp) cc_final: 0.9089 (mmp)
REVERT: A   98 MET cc_start: 0.9088 (tpp) cc_final: 0.8634 (tpt)
REVERT: A  111 MET cc_start: 0.8723 (tmm) cc_final: 0.8521 (tmm)
REVERT: A  160 MET cc_start: 0.9579 (mtm) cc_final: 0.9096 (mtt)
REVERT: A  196 MET cc_start: 0.9376 (tpp) cc_final: 0.7969 (tpp)
REVERT: A  200 MET cc_start: 0.9505 (tpp) cc_final: 0.9137 (mpp)
REVERT: A  244 MET cc_start: 0.9395 (mtt) cc_final: 0.8669 (mmt)
REVERT: A  276 MET cc_start: 0.8896 (ptm) cc_final: 0.8499 (ptm)
REVERT: A  524 ASP cc_start: 0.9405 (t0) cc_final: 0.9195 (m-30)
REVERT: B   98 MET cc_start: 0.9038 (ttm) cc_final: 0.8674 (tpt)
REVERT: B  111 MET cc_start: 0.9471 (OUTLIER) cc_final: 0.8922 (tmm)
REVERT: B  196 MET cc_start: 0.9489 (tpt) cc_final: 0.8059 (tpp)
REVERT: B  210 MET cc_start: 0.9202 (mmm) cc_final: 0.8925 (mmt)
REVERT: B  244 MET cc_start: 0.9726 (ttm) cc_final: 0.8999 (ttt)
  outliers start: 11
  outliers final: 4
  residues processed: 75
  average time/residue: 0.2081
  time to fit residues: 22.5998
Evaluate side-chains
  72 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  390 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 91 optimal weight:   20.0000
   chunk 83 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 54 optimal weight:   20.0000
   chunk 88 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 209 GLN
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 436 ASN
** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.033950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.023956 restraints weight = 85121.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.024753 restraints weight = 53416.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.025296 restraints weight = 39829.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9044  Z= 0.224
  Angle     :  0.578   9.076  12223  Z= 0.302
  Chirality :  0.041   0.200   1454
  Planarity :  0.004   0.040   1547
  Dihedral  :  3.813  18.455   1249
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.14 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 14.12 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.25), residues: 1146
  helix:  1.87 (0.19), residues: 752
  sheet:  1.53 (0.59), residues: 70
  loop : -0.36 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  10 
 HIS   0.005   0.001   HIS A 427 
 PHE   0.012   0.001   PHE B  56 
 TYR   0.009   0.001   TYR A 439 
 ARG   0.003   0.000   ARG B 517 

*********************** 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
  76 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9593 (tpp) cc_final: 0.9116 (mmp)
REVERT: A   98 MET cc_start: 0.9010 (tpp) cc_final: 0.8495 (tpt)
REVERT: A  111 MET cc_start: 0.8754 (tmm) cc_final: 0.8420 (tmm)
REVERT: A  160 MET cc_start: 0.9708 (mtm) cc_final: 0.9442 (mtt)
REVERT: A  196 MET cc_start: 0.9495 (tpp) cc_final: 0.9170 (tpt)
REVERT: A  276 MET cc_start: 0.8947 (ptm) cc_final: 0.8503 (ptm)
REVERT: A  402 MET cc_start: 0.9571 (ppp) cc_final: 0.9300 (ppp)
REVERT: A  460 MET cc_start: 0.9307 (mmm) cc_final: 0.8856 (mmm)
REVERT: B   98 MET cc_start: 0.9133 (ttm) cc_final: 0.8679 (tpp)
REVERT: B  111 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.8933 (tmm)
REVERT: B  160 MET cc_start: 0.9642 (ttm) cc_final: 0.9262 (mmt)
REVERT: B  196 MET cc_start: 0.9503 (tpt) cc_final: 0.8416 (tpp)
REVERT: B  200 MET cc_start: 0.8801 (mmm) cc_final: 0.7702 (mmm)
REVERT: B  210 MET cc_start: 0.9302 (mmm) cc_final: 0.8963 (mmt)
REVERT: B  244 MET cc_start: 0.9724 (ttm) cc_final: 0.8745 (ttt)
REVERT: B  402 MET cc_start: 0.9241 (ppp) cc_final: 0.8946 (ppp)
  outliers start: 8
  outliers final: 6
  residues processed: 72
  average time/residue: 0.2088
  time to fit residues: 21.8362
Evaluate side-chains
  70 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  390 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 92 optimal weight:    7.9990
   chunk 82 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 98 optimal weight:    0.3980
   chunk 61 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 GLN ** 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 = 0.3067 r_free = 0.3067 target = 0.034901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.025321 restraints weight = 82243.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.026143 restraints weight = 51480.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.026706 restraints weight = 37921.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9044  Z= 0.145
  Angle     :  0.534   9.200  12223  Z= 0.273
  Chirality :  0.040   0.127   1454
  Planarity :  0.003   0.039   1547
  Dihedral  :  3.624  15.176   1249
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.62 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 16.99 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.26), residues: 1146
  helix:  2.18 (0.19), residues: 742
  sheet:  1.61 (0.59), residues: 70
  loop : -0.44 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  10 
 HIS   0.004   0.001   HIS A 427 
 PHE   0.008   0.001   PHE B  56 
 TYR   0.007   0.001   TYR A 439 
 ARG   0.004   0.000   ARG B 569 

*********************** 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
  79 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9561 (tpp) cc_final: 0.9053 (mmp)
REVERT: A   98 MET cc_start: 0.8962 (tpp) cc_final: 0.8456 (tpt)
REVERT: A  160 MET cc_start: 0.9627 (mtm) cc_final: 0.9389 (mtt)
REVERT: A  196 MET cc_start: 0.9539 (tpp) cc_final: 0.8357 (tpp)
REVERT: A  200 MET cc_start: 0.9550 (tpp) cc_final: 0.9045 (mmm)
REVERT: A  244 MET cc_start: 0.9445 (mtt) cc_final: 0.8408 (mmt)
REVERT: A  276 MET cc_start: 0.8952 (ptm) cc_final: 0.8376 (ptm)
REVERT: A  402 MET cc_start: 0.9503 (ppp) cc_final: 0.9197 (ppp)
REVERT: B   98 MET cc_start: 0.9077 (ttm) cc_final: 0.8839 (ttm)
REVERT: B  196 MET cc_start: 0.9500 (tpt) cc_final: 0.8339 (tpp)
REVERT: B  200 MET cc_start: 0.9055 (mmm) cc_final: 0.7980 (mmm)
REVERT: B  210 MET cc_start: 0.9319 (mmm) cc_final: 0.9026 (mmt)
REVERT: B  244 MET cc_start: 0.9752 (ttm) cc_final: 0.8565 (ttt)
REVERT: B  312 MET cc_start: 0.9297 (tpp) cc_final: 0.8623 (mmm)
REVERT: B  402 MET cc_start: 0.9209 (ppp) cc_final: 0.8940 (ppp)
REVERT: B  460 MET cc_start: 0.9071 (mmm) cc_final: 0.8825 (tpp)
  outliers start: 10
  outliers final: 4
  residues processed: 76
  average time/residue: 0.2123
  time to fit residues: 23.9450
Evaluate side-chains
  68 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  543 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 111 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0870
   chunk 77 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:   10.0000
   chunk 103 optimal weight:    0.1980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 GLN ** 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 = 0.3054 r_free = 0.3054 target = 0.034931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.025050 restraints weight = 80362.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.025884 restraints weight = 50575.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.026451 restraints weight = 37497.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.2797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9044  Z= 0.140
  Angle     :  0.535   9.218  12223  Z= 0.271
  Chirality :  0.040   0.143   1454
  Planarity :  0.003   0.038   1547
  Dihedral  :  3.592  16.689   1249
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.53 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 17.91 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.26), residues: 1146
  helix:  2.36 (0.19), residues: 728
  sheet:  1.53 (0.59), residues: 70
  loop : -0.31 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  10 
 HIS   0.004   0.001   HIS A 427 
 PHE   0.008   0.001   PHE B 429 
 TYR   0.025   0.001   TYR A 572 
 ARG   0.003   0.000   ARG A 569 

*********************** 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
  73 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9634 (tpp) cc_final: 0.9112 (mmp)
REVERT: A   98 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8579 (tpt)
REVERT: A  111 MET cc_start: 0.8784 (tmm) cc_final: 0.8515 (tmm)
REVERT: A  160 MET cc_start: 0.9656 (mtm) cc_final: 0.9403 (mtt)
REVERT: A  196 MET cc_start: 0.9572 (tpp) cc_final: 0.9264 (tpt)
REVERT: A  276 MET cc_start: 0.8983 (ptm) cc_final: 0.8466 (ptm)
REVERT: A  312 MET cc_start: 0.9279 (mmm) cc_final: 0.8861 (tpp)
REVERT: A  402 MET cc_start: 0.9519 (ppp) cc_final: 0.9239 (ppp)
REVERT: A  460 MET cc_start: 0.9141 (mmm) cc_final: 0.8844 (mmm)
REVERT: B   98 MET cc_start: 0.9114 (ttm) cc_final: 0.8836 (ttm)
REVERT: B  111 MET cc_start: 0.9545 (ppp) cc_final: 0.9031 (tmm)
REVERT: B  196 MET cc_start: 0.9475 (tpt) cc_final: 0.8220 (tpp)
REVERT: B  200 MET cc_start: 0.9078 (mmm) cc_final: 0.7901 (mmm)
REVERT: B  210 MET cc_start: 0.9357 (mmm) cc_final: 0.9134 (mmm)
REVERT: B  244 MET cc_start: 0.9800 (ttm) cc_final: 0.8675 (ttt)
REVERT: B  312 MET cc_start: 0.9312 (tpp) cc_final: 0.8571 (mmm)
REVERT: B  402 MET cc_start: 0.9181 (ppp) cc_final: 0.8916 (ppp)
REVERT: B  460 MET cc_start: 0.9057 (mmm) cc_final: 0.8839 (tpp)
  outliers start: 7
  outliers final: 5
  residues processed: 70
  average time/residue: 0.1732
  time to fit residues: 18.5380
Evaluate side-chains
  68 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  543 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 11 optimal weight:    8.9990
   chunk 93 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 76 optimal weight:    9.9990
   chunk 46 optimal weight:    7.9990
   chunk 35 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 GLN ** 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 = 0.3026 r_free = 0.3026 target = 0.033984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.024111 restraints weight = 82393.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.024911 restraints weight = 52188.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.025455 restraints weight = 38935.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9044  Z= 0.182
  Angle     :  0.550   8.936  12223  Z= 0.282
  Chirality :  0.040   0.153   1454
  Planarity :  0.003   0.038   1547
  Dihedral  :  3.609  15.120   1249
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.79 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 17.50 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.25 (0.26), residues: 1146
  helix:  2.28 (0.19), residues: 732
  sheet:  1.53 (0.60), residues: 70
  loop : -0.24 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  10 
 HIS   0.006   0.001   HIS A 562 
 PHE   0.009   0.001   PHE B 429 
 TYR   0.017   0.001   TYR A 572 
 ARG   0.003   0.000   ARG A 101 

*********************** 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
  75 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9613 (tpp) cc_final: 0.9170 (mmp)
REVERT: A   98 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8575 (tpt)
REVERT: A  111 MET cc_start: 0.8923 (tmm) cc_final: 0.8593 (tmm)
REVERT: A  196 MET cc_start: 0.9609 (tpp) cc_final: 0.8995 (tpp)
REVERT: A  200 MET cc_start: 0.9545 (tpp) cc_final: 0.9073 (tpp)
REVERT: A  223 GLN cc_start: 0.9444 (OUTLIER) cc_final: 0.9116 (mp10)
REVERT: A  276 MET cc_start: 0.8954 (ptm) cc_final: 0.8490 (ptm)
REVERT: A  402 MET cc_start: 0.9553 (ppp) cc_final: 0.9278 (ppp)
REVERT: A  460 MET cc_start: 0.9212 (mmm) cc_final: 0.8896 (mmm)
REVERT: B   98 MET cc_start: 0.9114 (ttm) cc_final: 0.8829 (ttm)
REVERT: B  196 MET cc_start: 0.9447 (tpt) cc_final: 0.8117 (tpp)
REVERT: B  200 MET cc_start: 0.9121 (mmm) cc_final: 0.7892 (mmm)
REVERT: B  210 MET cc_start: 0.9362 (mmm) cc_final: 0.9149 (mmm)
REVERT: B  244 MET cc_start: 0.9803 (ttm) cc_final: 0.8711 (ttm)
REVERT: B  312 MET cc_start: 0.9347 (tpp) cc_final: 0.8608 (mmm)
REVERT: B  402 MET cc_start: 0.9221 (ppp) cc_final: 0.8726 (ppp)
  outliers start: 14
  outliers final: 8
  residues processed: 70
  average time/residue: 0.1764
  time to fit residues: 19.0014
Evaluate side-chains
  70 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  543 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 90 optimal weight:    7.9990
   chunk 95 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 100 optimal weight:    0.8980
   chunk 68 optimal weight:    8.9990
   chunk 65 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 GLN ** 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 = 0.3046 r_free = 0.3046 target = 0.034520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.024712 restraints weight = 82410.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.025536 restraints weight = 51346.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.026105 restraints weight = 38002.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
moved from start:          0.3161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9044  Z= 0.150
  Angle     :  0.555  10.239  12223  Z= 0.278
  Chirality :  0.040   0.181   1454
  Planarity :  0.003   0.036   1547
  Dihedral  :  3.602  16.565   1249
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.44 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 17.91 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.26), residues: 1146
  helix:  2.30 (0.19), residues: 734
  sheet:  1.56 (0.61), residues: 70
  loop : -0.19 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  10 
 HIS   0.005   0.001   HIS A 562 
 PHE   0.006   0.001   PHE B 220 
 TYR   0.014   0.001   TYR A 572 
 ARG   0.003   0.000   ARG A 101 

*********************** 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
  78 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9612 (tpp) cc_final: 0.9138 (mmp)
REVERT: A   98 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8629 (tpt)
REVERT: A  111 MET cc_start: 0.8939 (tmm) cc_final: 0.8545 (tmm)
REVERT: A  196 MET cc_start: 0.9630 (tpp) cc_final: 0.9041 (tpp)
REVERT: A  200 MET cc_start: 0.9537 (tpp) cc_final: 0.9106 (tpp)
REVERT: A  276 MET cc_start: 0.8952 (ptm) cc_final: 0.8511 (ptm)
REVERT: A  402 MET cc_start: 0.9580 (ppp) cc_final: 0.9314 (ppp)
REVERT: A  460 MET cc_start: 0.9193 (mmm) cc_final: 0.8876 (mmm)
REVERT: B   98 MET cc_start: 0.9102 (ttm) cc_final: 0.8766 (ttm)
REVERT: B  196 MET cc_start: 0.9445 (tpt) cc_final: 0.8118 (tpp)
REVERT: B  200 MET cc_start: 0.9176 (mmm) cc_final: 0.8077 (mmm)
REVERT: B  244 MET cc_start: 0.9809 (ttm) cc_final: 0.8763 (ttm)
REVERT: B  312 MET cc_start: 0.9315 (tpp) cc_final: 0.8595 (mmm)
REVERT: B  402 MET cc_start: 0.9205 (ppp) cc_final: 0.8702 (ppp)
REVERT: B  456 MET cc_start: 0.9642 (ptp) cc_final: 0.9231 (ptp)
  outliers start: 15
  outliers final: 11
  residues processed: 74
  average time/residue: 0.1649
  time to fit residues: 18.7012
Evaluate side-chains
  73 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  543 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 103 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 81 optimal weight:    8.9990
   chunk 9 optimal weight:    0.7980
   chunk 113 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 ASN
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 202 GLN
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.033082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.023415 restraints weight = 86066.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.024177 restraints weight = 54702.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.024698 restraints weight = 41031.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8820
moved from start:          0.3351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9044  Z= 0.236
  Angle     :  0.613  10.459  12223  Z= 0.311
  Chirality :  0.041   0.185   1454
  Planarity :  0.004   0.038   1547
  Dihedral  :  3.738  17.550   1249
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.32 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.40 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.25), residues: 1146
  helix:  2.07 (0.19), residues: 744
  sheet:  1.49 (0.60), residues: 70
  loop : -0.20 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  66 
 HIS   0.005   0.001   HIS A 427 
 PHE   0.012   0.001   PHE B 429 
 TYR   0.015   0.001   TYR A 572 
 ARG   0.004   0.000   ARG B 101 

*********************** 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
  75 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 1.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9593 (tpp) cc_final: 0.9201 (mmp)
REVERT: A   98 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8524 (tpt)
REVERT: A  196 MET cc_start: 0.9641 (tpp) cc_final: 0.9373 (tpp)
REVERT: A  200 MET cc_start: 0.9531 (tpp) cc_final: 0.9283 (tpp)
REVERT: A  223 GLN cc_start: 0.9405 (OUTLIER) cc_final: 0.9132 (mp10)
REVERT: A  276 MET cc_start: 0.8896 (ptm) cc_final: 0.8448 (ptm)
REVERT: A  402 MET cc_start: 0.9568 (ppp) cc_final: 0.9289 (ppp)
REVERT: B   98 MET cc_start: 0.9120 (ttm) cc_final: 0.8796 (ttm)
REVERT: B  196 MET cc_start: 0.9434 (tpt) cc_final: 0.8095 (tpp)
REVERT: B  200 MET cc_start: 0.9151 (mmm) cc_final: 0.8102 (mmm)
REVERT: B  244 MET cc_start: 0.9781 (ttm) cc_final: 0.8764 (ttm)
REVERT: B  312 MET cc_start: 0.9370 (tpp) cc_final: 0.8636 (mmm)
REVERT: B  402 MET cc_start: 0.9266 (ppp) cc_final: 0.8778 (ppp)
REVERT: B  456 MET cc_start: 0.9654 (ptp) cc_final: 0.9277 (ptp)
  outliers start: 18
  outliers final: 11
  residues processed: 72
  average time/residue: 0.2607
  time to fit residues: 27.8880
Evaluate side-chains
  70 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 1.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  479 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 54 optimal weight:    8.9990
   chunk 83 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 436 ASN
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.033232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2596 r_free = 0.2596 target = 0.023564 restraints weight = 83312.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.024322 restraints weight = 53126.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.024839 restraints weight = 39992.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8811
moved from start:          0.3448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9044  Z= 0.214
  Angle     :  0.644  11.566  12223  Z= 0.316
  Chirality :  0.041   0.186   1454
  Planarity :  0.003   0.034   1547
  Dihedral  :  3.795  20.659   1249
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.97 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 18.42 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.25), residues: 1146
  helix:  1.94 (0.19), residues: 756
  sheet:  1.53 (0.60), residues: 70
  loop : -0.38 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  10 
 HIS   0.005   0.001   HIS A 427 
 PHE   0.010   0.001   PHE B  56 
 TYR   0.013   0.001   TYR A 572 
 ARG   0.004   0.000   ARG B 101 

*********************** 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
  75 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 1.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9565 (tpp) cc_final: 0.9216 (mmp)
REVERT: A   98 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8530 (tpt)
REVERT: A  196 MET cc_start: 0.9652 (tpp) cc_final: 0.9391 (tpp)
REVERT: A  200 MET cc_start: 0.9535 (tpp) cc_final: 0.9272 (tpp)
REVERT: A  223 GLN cc_start: 0.9402 (OUTLIER) cc_final: 0.9134 (mp10)
REVERT: A  276 MET cc_start: 0.8897 (ptm) cc_final: 0.8440 (ptm)
REVERT: A  402 MET cc_start: 0.9567 (ppp) cc_final: 0.9295 (ppp)
REVERT: A  460 MET cc_start: 0.9259 (mmm) cc_final: 0.8868 (mmm)
REVERT: B   98 MET cc_start: 0.9134 (ttm) cc_final: 0.8806 (ttm)
REVERT: B  196 MET cc_start: 0.9444 (tpt) cc_final: 0.8075 (tpp)
REVERT: B  200 MET cc_start: 0.9185 (mmm) cc_final: 0.8237 (mmm)
REVERT: B  244 MET cc_start: 0.9786 (ttm) cc_final: 0.8584 (ttt)
REVERT: B  312 MET cc_start: 0.9396 (tpp) cc_final: 0.8675 (mmm)
REVERT: B  402 MET cc_start: 0.9311 (ppp) cc_final: 0.8902 (ppp)
REVERT: B  456 MET cc_start: 0.9672 (ptp) cc_final: 0.9344 (ptp)
REVERT: B  460 MET cc_start: 0.8974 (mmm) cc_final: 0.8729 (mmm)
  outliers start: 17
  outliers final: 13
  residues processed: 72
  average time/residue: 0.2881
  time to fit residues: 33.2507
Evaluate side-chains
  73 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 1.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  479 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 61 optimal weight:    0.0470
   chunk 112 optimal weight:   30.0000
   chunk 35 optimal weight:   10.0000
   chunk 55 optimal weight:   20.0000
   chunk 81 optimal weight:    0.7980
   chunk 98 optimal weight:    5.9990
   chunk 113 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 44 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    1.4882

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

Flipped N/Q/H residues before XYZ refinement:
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 GLN ** 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 = 0.3015 r_free = 0.3015 target = 0.033563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.023915 restraints weight = 83785.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.024724 restraints weight = 52387.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.025284 restraints weight = 38689.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8786
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9044  Z= 0.184
  Angle     :  0.644  12.800  12223  Z= 0.312
  Chirality :  0.041   0.179   1454
  Planarity :  0.003   0.035   1547
  Dihedral  :  3.754  19.673   1249
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.88 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 18.73 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.25), residues: 1146
  helix:  1.98 (0.19), residues: 756
  sheet:  1.59 (0.60), residues: 70
  loop : -0.36 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  10 
 HIS   0.005   0.001   HIS A 562 
 PHE   0.009   0.001   PHE B 220 
 TYR   0.012   0.001   TYR A 572 
 ARG   0.003   0.000   ARG A 101 

********************** 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
  73 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9579 (tpp) cc_final: 0.9215 (mmp)
REVERT: A   98 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8508 (tpt)
REVERT: A  196 MET cc_start: 0.9645 (tpp) cc_final: 0.9388 (tpp)
REVERT: A  200 MET cc_start: 0.9498 (tpp) cc_final: 0.9249 (tpp)
REVERT: A  223 GLN cc_start: 0.9457 (OUTLIER) cc_final: 0.9213 (mp10)
REVERT: A  276 MET cc_start: 0.8890 (ptm) cc_final: 0.8441 (ptm)
REVERT: A  402 MET cc_start: 0.9573 (ppp) cc_final: 0.9301 (ppp)
REVERT: A  460 MET cc_start: 0.9280 (mmm) cc_final: 0.8893 (mmm)
REVERT: B   98 MET cc_start: 0.9124 (ttm) cc_final: 0.8791 (ttm)
REVERT: B  196 MET cc_start: 0.9412 (tpt) cc_final: 0.8532 (tpp)
REVERT: B  244 MET cc_start: 0.9806 (ttm) cc_final: 0.8746 (ttt)
REVERT: B  312 MET cc_start: 0.9394 (tpp) cc_final: 0.8671 (mmm)
REVERT: B  402 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.8961 (ppp)
REVERT: B  460 MET cc_start: 0.9061 (mmm) cc_final: 0.8513 (mmm)
  outliers start: 15
  outliers final: 12
  residues processed: 69
  average time/residue: 0.1788
  time to fit residues: 18.9424
Evaluate side-chains
  72 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  479 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 106 optimal weight:    7.9990
   chunk 93 optimal weight:    5.9990
   chunk 58 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 10 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 GLN ** 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 = 0.3027 r_free = 0.3027 target = 0.033887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.024206 restraints weight = 83144.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.025020 restraints weight = 52181.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2669 r_free = 0.2669 target = 0.025585 restraints weight = 38755.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9044  Z= 0.167
  Angle     :  0.643  13.395  12223  Z= 0.311
  Chirality :  0.041   0.184   1454
  Planarity :  0.003   0.035   1547
  Dihedral  :  3.728  19.035   1249
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.71 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 18.94 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.25), residues: 1146
  helix:  2.01 (0.19), residues: 756
  sheet:  1.69 (0.61), residues: 70
  loop : -0.35 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  10 
 HIS   0.004   0.001   HIS A 562 
 PHE   0.012   0.001   PHE B 462 
 TYR   0.011   0.001   TYR A 572 
 ARG   0.002   0.000   ARG A 102 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2590.58 seconds
wall clock time: 47 minutes 5.73 seconds (2825.73 seconds total)