Starting phenix.real_space_refine
on Tue Mar  3 19:41:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r8c_24315/03_2026/7r8c_24315.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r8c_24315/03_2026/7r8c_24315.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r8c_24315/03_2026/7r8c_24315.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r8c_24315/03_2026/7r8c_24315.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r8c_24315/03_2026/7r8c_24315.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r8c_24315/03_2026/7r8c_24315.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      68      5.16       5
     C    5540      2.51       5
     N    1412      2.21       5
     O    1518      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8538
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 545, 4269
          Classifications: {'peptide': 545}
          Link IDs: {'PTRANS': 18, 'TRANS': 526}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 545, 4269
          Classifications: {'peptide': 545}
          Link IDs: {'PTRANS': 18, 'TRANS': 526}
          Chain breaks: 2
  Time building chain proxies: 1.93, per 1000 atoms: 0.23
  Number of scatterers: 8538
  At special positions: 0
  Unit cell: (107.457, 75.803, 119.952, 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      68     16.00
     O    1518      8.00
     N    1412      7.00
     C    5540      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 611 " - pdb=" SG  CYS A 617 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 611 " - pdb=" SG  CYS B 617 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 233.1 milliseconds
  

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2016

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 4 sheets defined
      63.3% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 123 through 132
      removed outlier: 3.613A  pdb=" N   MET A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 158
      removed outlier: 3.699A  pdb=" N   LYS A 157 " --> pdb=" O   ARG A 153 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL A 158 " --> pdb=" O   CYS A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 186
    Processing helix  chain 'A' and resid 189 through 205
    Processing helix  chain 'A' and resid 206 through 210
    Processing helix  chain 'A' and resid 213 through 217
    Processing helix  chain 'A' and resid 218 through 230
    Processing helix  chain 'A' and resid 248 through 265
    Processing helix  chain 'A' and resid 277 through 283
      removed outlier: 3.840A  pdb=" N   LEU A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 303
    Processing helix  chain 'A' and resid 304 through 311
      removed outlier: 3.642A  pdb=" N   LEU A 311 " --> pdb=" O   TYR A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 330
    Processing helix  chain 'A' and resid 336 through 346
    Processing helix  chain 'A' and resid 390 through 407
      removed outlier: 3.740A  pdb=" N   ASP A 407 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 429
      removed outlier: 3.611A  pdb=" N   ILE A 415 " --> pdb=" O   THR A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 465
      removed outlier: 3.624A  pdb=" N   PHE A 448 " --> pdb=" O   GLY A 444 " (cutoff:3.500A)
      Proline residue:  A 460  - end of helix
    Processing helix  chain 'A' and resid 469 through 478
      removed outlier: 3.706A  pdb=" N   ASN A 478 " --> pdb=" O   ARG A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 511
      Proline residue:  A 496  - end of helix
      Proline residue:  A 502  - end of helix
      removed outlier: 3.854A  pdb=" N   TRP A 511 " --> pdb=" O   SER A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 547
    Processing helix  chain 'A' and resid 549 through 567
      Proline residue:  A 558  - end of helix
      Proline residue:  A 563  - end of helix
      removed outlier: 3.630A  pdb=" N   LEU A 566 " --> pdb=" O   ILE A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 587
      removed outlier: 3.788A  pdb=" N   ILE A 587 " --> pdb=" O   TRP A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 602
      removed outlier: 3.551A  pdb=" N   TYR A 592 " --> pdb=" O   SER A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 622
      removed outlier: 4.294A  pdb=" N   SER A 622 " --> pdb=" O   PHE A 619 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 619 through 622'
    Processing helix  chain 'A' and resid 623 through 629
    Processing helix  chain 'A' and resid 635 through 665
      removed outlier: 3.888A  pdb=" N   ASP A 639 " --> pdb=" O   LYS A 635 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 132
      removed outlier: 3.614A  pdb=" N   MET B 128 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 158
      removed outlier: 3.700A  pdb=" N   LYS B 157 " --> pdb=" O   ARG B 153 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 186
    Processing helix  chain 'B' and resid 189 through 205
    Processing helix  chain 'B' and resid 206 through 210
    Processing helix  chain 'B' and resid 213 through 217
    Processing helix  chain 'B' and resid 218 through 230
    Processing helix  chain 'B' and resid 248 through 265
    Processing helix  chain 'B' and resid 277 through 283
      removed outlier: 3.840A  pdb=" N   LEU B 283 " --> pdb=" O   LYS B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 303
    Processing helix  chain 'B' and resid 304 through 311
      removed outlier: 3.640A  pdb=" N   LEU B 311 " --> pdb=" O   TYR B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 330
    Processing helix  chain 'B' and resid 336 through 346
    Processing helix  chain 'B' and resid 390 through 407
      removed outlier: 3.739A  pdb=" N   ASP B 407 " --> pdb=" O   SER B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 429
      removed outlier: 3.610A  pdb=" N   ILE B 415 " --> pdb=" O   THR B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 465
      removed outlier: 3.624A  pdb=" N   PHE B 448 " --> pdb=" O   GLY B 444 " (cutoff:3.500A)
      Proline residue:  B 460  - end of helix
    Processing helix  chain 'B' and resid 469 through 478
      removed outlier: 3.707A  pdb=" N   ASN B 478 " --> pdb=" O   ARG B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 511
      Proline residue:  B 496  - end of helix
      Proline residue:  B 502  - end of helix
      removed outlier: 3.855A  pdb=" N   TRP B 511 " --> pdb=" O   SER B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 547
    Processing helix  chain 'B' and resid 549 through 567
      Proline residue:  B 558  - end of helix
      Proline residue:  B 563  - end of helix
      removed outlier: 3.630A  pdb=" N   LEU B 566 " --> pdb=" O   ILE B 562 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 582 through 587
      removed outlier: 3.788A  pdb=" N   ILE B 587 " --> pdb=" O   TRP B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 588 through 602
      removed outlier: 3.551A  pdb=" N   TYR B 592 " --> pdb=" O   SER B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 619 through 622
      removed outlier: 4.295A  pdb=" N   SER B 622 " --> pdb=" O   PHE B 619 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 619 through 622'
    Processing helix  chain 'B' and resid 623 through 629
    Processing helix  chain 'B' and resid 635 through 665
      removed outlier: 3.888A  pdb=" N   ASP B 639 " --> pdb=" O   LYS B 635 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 108
      removed outlier: 5.375A  pdb=" N   LYS A 102 " --> pdb=" O   TYR A  84 " (cutoff:3.500A)
      removed outlier: 5.247A  pdb=" N   TYR A  84 " --> pdb=" O   LYS A 102 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   GLY A 106 " --> pdb=" O   ARG A  80 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   ARG A  80 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   PHE A 108 " --> pdb=" O   GLU A  78 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   GLU A  78 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ARG A  80 " --> pdb=" O   ALA A 142 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ALA A 142 " --> pdb=" O   ARG A  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 162
      removed outlier: 6.159A  pdb=" N   MET A 238 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   THR A 272 " --> pdb=" O   MET A 238 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   PHE A 240 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   LEU A 113 " --> pdb=" O   GLN A 286 " (cutoff:3.500A)
      removed outlier: 8.247A  pdb=" N   TYR A 288 " --> pdb=" O   LEU A 113 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ALA A 115 " --> pdb=" O   TYR A 288 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   LEU A 290 " --> pdb=" O   ALA A 115 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   MET A 117 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   LEU A 287 " --> pdb=" O   ARG A 298 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   ARG A 298 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   VAL A 289 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 108
      removed outlier: 5.374A  pdb=" N   LYS B 102 " --> pdb=" O   TYR B  84 " (cutoff:3.500A)
      removed outlier: 5.245A  pdb=" N   TYR B  84 " --> pdb=" O   LYS B 102 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   GLY B 106 " --> pdb=" O   ARG B  80 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   ARG B  80 " --> pdb=" O   GLY B 106 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   PHE B 108 " --> pdb=" O   GLU B  78 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   GLU B  78 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ARG B  80 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ALA B 142 " --> pdb=" O   ARG B  80 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 162
      removed outlier: 6.159A  pdb=" N   MET B 238 " --> pdb=" O   ILE B 270 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   THR B 272 " --> pdb=" O   MET B 238 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   PHE B 240 " --> pdb=" O   THR B 272 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   LEU B 113 " --> pdb=" O   GLN B 286 " (cutoff:3.500A)
      removed outlier: 8.247A  pdb=" N   TYR B 288 " --> pdb=" O   LEU B 113 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ALA B 115 " --> pdb=" O   TYR B 288 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   LEU B 290 " --> pdb=" O   ALA B 115 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   MET B 117 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   LEU B 287 " --> pdb=" O   ARG B 298 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ARG B 298 " --> pdb=" O   LEU B 287 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   VAL B 289 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)

    470 hydrogen bonds defined for protein.
    1368 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.29

  Time building geometry restraints manager: 0.82 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: 2688
        1.34 -     1.46: 1765
        1.46 -     1.58: 4151
        1.58 -     1.69: 0
        1.69 -     1.81: 110
  Bond restraints: 8714
  Sorted by residual:
  bond pdb=" C   ILE B 562 "
       pdb=" N   PRO B 563 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.023 1.25e-02 6.40e+03 3.26e+00
  bond pdb=" C   ILE A 562 "
       pdb=" N   PRO A 563 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.023 1.25e-02 6.40e+03 3.25e+00
  bond pdb=" C   PHE B 465 "
       pdb=" N   PRO B 466 "
    ideal  model  delta    sigma   weight residual
    1.334  1.358 -0.024 2.34e-02 1.83e+03 1.05e+00
  bond pdb=" C   PHE A 465 "
       pdb=" N   PRO A 466 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.023 2.34e-02 1.83e+03 1.01e+00
  bond pdb=" N   VAL B 631 "
       pdb=" CA  VAL B 631 "
    ideal  model  delta    sigma   weight residual
    1.474  1.461  0.013 1.57e-02 4.06e+03 7.11e-01
  ... (remaining 8709 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 11352
        1.08 -     2.16: 335
        2.16 -     3.25: 57
        3.25 -     4.33: 20
        4.33 -     5.41: 14
  Bond angle restraints: 11778
  Sorted by residual:
  angle pdb=" C   GLN A 620 "
        pdb=" N   LYS A 621 "
        pdb=" CA  LYS A 621 "
      ideal   model   delta    sigma   weight residual
     123.91  129.10   -5.19 1.66e+00 3.63e-01 9.76e+00
  angle pdb=" C   GLN B 620 "
        pdb=" N   LYS B 621 "
        pdb=" CA  LYS B 621 "
      ideal   model   delta    sigma   weight residual
     123.91  129.09   -5.18 1.66e+00 3.63e-01 9.73e+00
  angle pdb=" N   PHE B 571 "
        pdb=" CA  PHE B 571 "
        pdb=" C   PHE B 571 "
      ideal   model   delta    sigma   weight residual
     114.04  110.76    3.28 1.24e+00 6.50e-01 6.98e+00
  angle pdb=" N   PHE A 571 "
        pdb=" CA  PHE A 571 "
        pdb=" C   PHE A 571 "
      ideal   model   delta    sigma   weight residual
     114.04  110.81    3.23 1.24e+00 6.50e-01 6.80e+00
  angle pdb=" C   ILE B 562 "
        pdb=" CA  ILE B 562 "
        pdb=" CB  ILE B 562 "
      ideal   model   delta    sigma   weight residual
     114.00  110.64    3.36 1.31e+00 5.83e-01 6.56e+00
  ... (remaining 11773 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.47: 4579
       14.47 -    28.94: 444
       28.94 -    43.41: 130
       43.41 -    57.88: 31
       57.88 -    72.35: 6
  Dihedral angle restraints: 5190
    sinusoidal: 2044
      harmonic: 3146
  Sorted by residual:
  dihedral pdb=" CA  ASP A 323 "
           pdb=" CB  ASP A 323 "
           pdb=" CG  ASP A 323 "
           pdb=" OD1 ASP A 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.71   53.71     1      2.00e+01 2.50e-03 9.79e+00
  dihedral pdb=" CA  ASP B 323 "
           pdb=" CB  ASP B 323 "
           pdb=" CG  ASP B 323 "
           pdb=" OD1 ASP B 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.70   53.70     1      2.00e+01 2.50e-03 9.79e+00
  dihedral pdb=" CA  PRO A 466 "
           pdb=" C   PRO A 466 "
           pdb=" N   LEU A 467 "
           pdb=" CA  LEU A 467 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.81   15.19     0      5.00e+00 4.00e-02 9.23e+00
  ... (remaining 5187 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 862
       0.027 -    0.055: 312
       0.055 -    0.082: 113
       0.082 -    0.110: 54
       0.110 -    0.137: 15
  Chirality restraints: 1356
  Sorted by residual:
  chirality pdb=" CA  ILE B 577 "
            pdb=" N   ILE B 577 "
            pdb=" C   ILE B 577 "
            pdb=" CB  ILE B 577 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.70e-01
  chirality pdb=" CA  ILE A 577 "
            pdb=" N   ILE A 577 "
            pdb=" C   ILE A 577 "
            pdb=" CB  ILE A 577 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.30e-01
  chirality pdb=" CA  LYS B 621 "
            pdb=" N   LYS B 621 "
            pdb=" C   LYS B 621 "
            pdb=" CB  LYS B 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 1353 not shown)

  Planarity restraints: 1474
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 456 "    0.008 2.00e-02 2.50e+03   1.59e-02 2.53e+00
        pdb=" C   ALA B 456 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   ALA B 456 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ALA B 457 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 456 "   -0.008 2.00e-02 2.50e+03   1.57e-02 2.48e+00
        pdb=" C   ALA A 456 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ALA A 456 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ALA A 457 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 465 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO B 466 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B 466 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 466 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1471 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 82
        2.64 -     3.20: 7866
        3.20 -     3.77: 13030
        3.77 -     4.33: 17371
        4.33 -     4.90: 29252
  Nonbonded interactions: 67601
  Sorted by model distance:
  nonbonded pdb=" CD2 LEU A 231 "
            pdb=" NH1 ARG A 267 "
     model   vdw
     2.073 3.540
  nonbonded pdb=" OE1 GLU A 475 "
            pdb=" OH  TYR A 481 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OE1 GLU B 475 "
            pdb=" OH  TYR B 481 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   ILE A 404 "
            pdb=" OG1 THR A 411 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   ILE B 404 "
            pdb=" OG1 THR B 411 "
     model   vdw
     2.250 3.040
  ... (remaining 67596 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  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:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.610
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
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      :  0.002   0.024   8716  Z= 0.110
  Angle     :  0.494   5.412  11782  Z= 0.296
  Chirality :  0.037   0.137   1356
  Planarity :  0.003   0.034   1474
  Dihedral  : 12.820  72.351   3168
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.43 %
    Favored  : 96.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.24), residues: 1078
  helix: -0.12 (0.20), residues: 630
  sheet: -1.34 (0.47), residues: 80
  loop : -2.66 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 651 
 TYR   0.006   0.001   TYR A 510 
 PHE   0.006   0.001   PHE B 646 
 TRP   0.002   0.000   TRP A 511 
 HIS   0.001   0.000   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00184 ( 8714)
  covalent geometry    : angle       0.49370 (11778)
  SS BOND              : bond        0.00011 (    2)
  SS BOND              : angle       0.68050 (    4)
  hydrogen bonds       : bond        0.14159 (  470)
  hydrogen bonds       : angle       5.25441 ( 1368)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 211
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A  155 PHE cc_start: 0.8611 (t80) cc_final: 0.8353 (t80)
REVERT: A  178 MET cc_start: 0.9440 (mmm) cc_final: 0.9233 (mmm)
REVERT: A  213 ARG cc_start: 0.8762 (mmt90) cc_final: 0.8488 (mmt90)
REVERT: A  230 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8416 (mm-30)
REVERT: A  238 MET cc_start: 0.8362 (mtp) cc_final: 0.8083 (mtp)
REVERT: A  500 MET cc_start: 0.8232 (tmm) cc_final: 0.7463 (tmm)
REVERT: A  511 TRP cc_start: 0.8076 (m100) cc_final: 0.7498 (t60)
REVERT: A  592 TYR cc_start: 0.8795 (m-80) cc_final: 0.8483 (m-80)
REVERT: A  595 GLU cc_start: 0.8259 (tt0) cc_final: 0.8048 (tt0)
REVERT: A  611 CYS cc_start: 0.4162 (t) cc_final: 0.3905 (t)
REVERT: A  628 GLU cc_start: 0.8938 (tp30) cc_final: 0.8697 (tp30)
REVERT: B  155 PHE cc_start: 0.8698 (t80) cc_final: 0.8400 (t80)
REVERT: B  176 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8261 (mt-10)
REVERT: B  178 MET cc_start: 0.9424 (mmm) cc_final: 0.9210 (mmm)
REVERT: B  213 ARG cc_start: 0.8761 (mmt90) cc_final: 0.8489 (mmt90)
REVERT: B  230 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8414 (mm-30)
REVERT: B  238 MET cc_start: 0.8378 (mtp) cc_final: 0.8091 (mtp)
REVERT: B  500 MET cc_start: 0.8241 (tmm) cc_final: 0.7460 (tmm)
REVERT: B  511 TRP cc_start: 0.8130 (m100) cc_final: 0.7511 (t60)
REVERT: B  570 PHE cc_start: 0.8335 (t80) cc_final: 0.7753 (t80)
REVERT: B  592 TYR cc_start: 0.8780 (m-80) cc_final: 0.8402 (m-80)
REVERT: B  595 GLU cc_start: 0.8252 (tt0) cc_final: 0.8046 (tt0)
REVERT: B  611 CYS cc_start: 0.4166 (t) cc_final: 0.3958 (t)
REVERT: B  628 GLU cc_start: 0.8968 (tp30) cc_final: 0.8736 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 213
  average time/residue: 0.0873
  time to fit residues: 26.1702
Evaluate side-chains
  127 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0010
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    1.4592

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

Flipped N/Q/H residues before XYZ refinement:
A 221 GLN
A 264 GLN
A 336 GLN
A 442 ASN
A 476 HIS
B 221 GLN
B 264 GLN
B 336 GLN
B 392 GLN
B 442 ASN
B 476 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.099029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.082496 restraints weight = 16593.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.085707 restraints weight = 8163.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.087910 restraints weight = 5015.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.089429 restraints weight = 3519.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.090416 restraints weight = 2719.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8716  Z= 0.147
  Angle     :  0.559   8.238  11782  Z= 0.277
  Chirality :  0.040   0.164   1356
  Planarity :  0.004   0.036   1474
  Dihedral  :  3.502  16.834   1188
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 11.80 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.26), residues: 1078
  helix:  1.29 (0.21), residues: 640
  sheet: -1.01 (0.46), residues: 80
  loop : -2.25 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 651 
 TYR   0.010   0.001   TYR B 510 
 PHE   0.020   0.001   PHE A 281 
 TRP   0.003   0.001   TRP A 480 
 HIS   0.010   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8714)
  covalent geometry    : angle       0.55952 (11778)
  SS BOND              : bond        0.00021 (    2)
  SS BOND              : angle       0.34093 (    4)
  hydrogen bonds       : bond        0.03109 (  470)
  hydrogen bonds       : angle       3.65816 ( 1368)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  155 PHE cc_start: 0.8831 (t80) cc_final: 0.8520 (t80)
REVERT: A  178 MET cc_start: 0.9432 (mmm) cc_final: 0.9219 (mmm)
REVERT: A  213 ARG cc_start: 0.8741 (mmt90) cc_final: 0.8438 (mmt90)
REVERT: A  454 MET cc_start: 0.8791 (ppp) cc_final: 0.8514 (tmm)
REVERT: A  475 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8332 (mm-30)
REVERT: A  500 MET cc_start: 0.8212 (tmm) cc_final: 0.7548 (tmm)
REVERT: A  511 TRP cc_start: 0.8021 (m100) cc_final: 0.7686 (t60)
REVERT: A  595 GLU cc_start: 0.8151 (tt0) cc_final: 0.7902 (tt0)
REVERT: A  628 GLU cc_start: 0.8710 (tp30) cc_final: 0.8481 (tp30)
REVERT: B  155 PHE cc_start: 0.8856 (t80) cc_final: 0.8515 (t80)
REVERT: B  178 MET cc_start: 0.9428 (mmm) cc_final: 0.9227 (mmm)
REVERT: B  454 MET cc_start: 0.8811 (ppp) cc_final: 0.8544 (tmm)
REVERT: B  475 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8328 (mm-30)
REVERT: B  500 MET cc_start: 0.8204 (tmm) cc_final: 0.7552 (tmm)
REVERT: B  511 TRP cc_start: 0.8084 (m100) cc_final: 0.7679 (t60)
REVERT: B  570 PHE cc_start: 0.8583 (t80) cc_final: 0.8327 (t80)
REVERT: B  592 TYR cc_start: 0.8693 (m-80) cc_final: 0.8425 (m-80)
REVERT: B  595 GLU cc_start: 0.8182 (tt0) cc_final: 0.7925 (tt0)
REVERT: B  628 GLU cc_start: 0.8738 (tp30) cc_final: 0.8400 (tp30)
  outliers start: 13
  outliers final: 8
  residues processed: 135
  average time/residue: 0.0762
  time to fit residues: 15.4332
Evaluate side-chains
  126 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   chunk 75 optimal weight:    0.0670
   chunk 11 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    1.7524

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

Flipped N/Q/H residues before XYZ refinement:
B 392 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.096654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.080111 restraints weight = 16694.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.083282 restraints weight = 7974.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.085499 restraints weight = 4827.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.086979 restraints weight = 3369.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.087860 restraints weight = 2608.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   8716  Z= 0.161
  Angle     :  0.553   6.789  11782  Z= 0.275
  Chirality :  0.040   0.162   1356
  Planarity :  0.004   0.039   1474
  Dihedral  :  3.638  18.908   1188
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 14.81 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.27), residues: 1078
  helix:  1.64 (0.21), residues: 640
  sheet: -0.97 (0.46), residues: 82
  loop : -1.92 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 651 
 TYR   0.018   0.001   TYR A 592 
 PHE   0.016   0.001   PHE B 281 
 TRP   0.004   0.001   TRP A 480 
 HIS   0.009   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 8714)
  covalent geometry    : angle       0.55284 (11778)
  SS BOND              : bond        0.00316 (    2)
  SS BOND              : angle       1.30386 (    4)
  hydrogen bonds       : bond        0.03086 (  470)
  hydrogen bonds       : angle       3.57923 ( 1368)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  155 PHE cc_start: 0.9042 (t80) cc_final: 0.8737 (t80)
REVERT: A  179 MET cc_start: 0.8995 (mmm) cc_final: 0.8654 (mmm)
REVERT: A  500 MET cc_start: 0.8215 (tmm) cc_final: 0.7496 (tmm)
REVERT: A  628 GLU cc_start: 0.8793 (tp30) cc_final: 0.8446 (tp30)
REVERT: B  155 PHE cc_start: 0.9080 (t80) cc_final: 0.8755 (t80)
REVERT: B  178 MET cc_start: 0.9473 (mmm) cc_final: 0.9236 (mmm)
REVERT: B  179 MET cc_start: 0.9003 (mmm) cc_final: 0.8689 (mmm)
REVERT: B  500 MET cc_start: 0.8207 (tmm) cc_final: 0.7496 (tmm)
REVERT: B  595 GLU cc_start: 0.8214 (tt0) cc_final: 0.7984 (tt0)
REVERT: B  628 GLU cc_start: 0.8811 (tp30) cc_final: 0.8484 (tp30)
  outliers start: 25
  outliers final: 16
  residues processed: 141
  average time/residue: 0.0842
  time to fit residues: 17.2611
Evaluate side-chains
  133 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  450 MET
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  645 ILE
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    4.9990
   chunk 105 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   overall best weight:    2.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.094944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.078283 restraints weight = 17122.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.081309 restraints weight = 8441.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.083431 restraints weight = 5220.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.084899 restraints weight = 3704.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.085882 restraints weight = 2894.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8716  Z= 0.195
  Angle     :  0.584   8.417  11782  Z= 0.289
  Chirality :  0.041   0.164   1356
  Planarity :  0.004   0.040   1474
  Dihedral  :  3.786  20.762   1188
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 15.02 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.27), residues: 1078
  helix:  1.65 (0.21), residues: 656
  sheet: -1.01 (0.48), residues: 82
  loop : -1.81 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 213 
 TYR   0.024   0.001   TYR B 592 
 PHE   0.013   0.002   PHE A 281 
 TRP   0.004   0.001   TRP A 480 
 HIS   0.009   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 8714)
  covalent geometry    : angle       0.58365 (11778)
  SS BOND              : bond        0.00291 (    2)
  SS BOND              : angle       1.46183 (    4)
  hydrogen bonds       : bond        0.03217 (  470)
  hydrogen bonds       : angle       3.60321 ( 1368)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 118
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8895 (mmm) cc_final: 0.8568 (mmm)
REVERT: A  500 MET cc_start: 0.8217 (tmm) cc_final: 0.7549 (tmm)
REVERT: A  628 GLU cc_start: 0.8711 (tp30) cc_final: 0.8285 (tm-30)
REVERT: B  179 MET cc_start: 0.8901 (mmm) cc_final: 0.8600 (mmm)
REVERT: B  500 MET cc_start: 0.8196 (tmm) cc_final: 0.7523 (tmm)
REVERT: B  512 MET cc_start: 0.9007 (ttm) cc_final: 0.8752 (ttt)
REVERT: B  628 GLU cc_start: 0.8744 (tp30) cc_final: 0.8455 (tp30)
  outliers start: 33
  outliers final: 26
  residues processed: 132
  average time/residue: 0.0811
  time to fit residues: 15.6747
Evaluate side-chains
  138 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  450 MET
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  572 VAL
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  645 ILE
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 13 optimal weight:    8.9990
   chunk 68 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 101 optimal weight:    0.7980
   chunk 107 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 19 optimal weight:    6.9990
   chunk 85 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 515 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 = 0.3304 r_free = 0.3304 target = 0.095740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.078728 restraints weight = 16705.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.081861 restraints weight = 8381.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.084022 restraints weight = 5211.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.085536 restraints weight = 3722.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.086397 restraints weight = 2911.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8716  Z= 0.119
  Angle     :  0.539   8.398  11782  Z= 0.264
  Chirality :  0.039   0.162   1356
  Planarity :  0.003   0.041   1474
  Dihedral  :  3.679  20.309   1188
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 18.03 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.27), residues: 1078
  helix:  1.87 (0.21), residues: 654
  sheet: -0.93 (0.49), residues: 82
  loop : -1.70 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 213 
 TYR   0.016   0.001   TYR B 592 
 PHE   0.013   0.001   PHE A 281 
 TRP   0.005   0.001   TRP B 480 
 HIS   0.007   0.001   HIS B 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8714)
  covalent geometry    : angle       0.53826 (11778)
  SS BOND              : bond        0.00344 (    2)
  SS BOND              : angle       1.23877 (    4)
  hydrogen bonds       : bond        0.02967 (  470)
  hydrogen bonds       : angle       3.47173 ( 1368)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8796 (mmm) cc_final: 0.8561 (mmm)
REVERT: A  500 MET cc_start: 0.8225 (tmm) cc_final: 0.7572 (tmm)
REVERT: A  628 GLU cc_start: 0.8642 (tp30) cc_final: 0.8240 (tm-30)
REVERT: B  179 MET cc_start: 0.8852 (mmm) cc_final: 0.8615 (mmm)
REVERT: B  500 MET cc_start: 0.8227 (tmm) cc_final: 0.7572 (tmm)
REVERT: B  628 GLU cc_start: 0.8669 (tp30) cc_final: 0.8381 (tp30)
  outliers start: 23
  outliers final: 19
  residues processed: 130
  average time/residue: 0.0784
  time to fit residues: 15.1372
Evaluate side-chains
  130 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  450 MET
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 105 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 107 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 442 ASN ** 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 = 0.3284 r_free = 0.3284 target = 0.094302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.077553 restraints weight = 16722.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.080587 restraints weight = 8377.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.082698 restraints weight = 5217.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.083985 restraints weight = 3725.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.085064 restraints weight = 2956.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8716  Z= 0.160
  Angle     :  0.567   7.450  11782  Z= 0.279
  Chirality :  0.041   0.167   1356
  Planarity :  0.003   0.042   1474
  Dihedral  :  3.755  20.555   1188
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 16.95 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.27), residues: 1078
  helix:  1.94 (0.21), residues: 656
  sheet: -0.91 (0.51), residues: 82
  loop : -1.59 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 213 
 TYR   0.014   0.001   TYR B 592 
 PHE   0.013   0.001   PHE B 284 
 TRP   0.005   0.001   TRP A 583 
 HIS   0.012   0.001   HIS B 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 8714)
  covalent geometry    : angle       0.56683 (11778)
  SS BOND              : bond        0.00053 (    2)
  SS BOND              : angle       1.23187 (    4)
  hydrogen bonds       : bond        0.03085 (  470)
  hydrogen bonds       : angle       3.50593 ( 1368)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 110
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8762 (mmm) cc_final: 0.8556 (mmm)
REVERT: A  500 MET cc_start: 0.8223 (tmm) cc_final: 0.7563 (tmm)
REVERT: A  628 GLU cc_start: 0.8644 (tp30) cc_final: 0.8264 (tm-30)
REVERT: B  179 MET cc_start: 0.8840 (mmm) cc_final: 0.8608 (mmm)
REVERT: B  500 MET cc_start: 0.8222 (tmm) cc_final: 0.7559 (tmm)
REVERT: B  628 GLU cc_start: 0.8666 (tp30) cc_final: 0.8279 (tm-30)
  outliers start: 32
  outliers final: 28
  residues processed: 127
  average time/residue: 0.0790
  time to fit residues: 14.9070
Evaluate side-chains
  137 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  450 MET
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  617 CYS
Chi-restraints excluded: chain B residue  645 ILE
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 81 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 104 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 442 ASN
** B 442 ASN ** 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 = 0.3267 r_free = 0.3267 target = 0.093182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.076573 restraints weight = 17058.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.079600 restraints weight = 8478.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.081692 restraints weight = 5244.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.083142 restraints weight = 3728.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.084013 restraints weight = 2915.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   8716  Z= 0.175
  Angle     :  0.577   7.667  11782  Z= 0.285
  Chirality :  0.041   0.167   1356
  Planarity :  0.004   0.042   1474
  Dihedral  :  3.846  21.242   1188
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 16.85 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.27), residues: 1078
  helix:  2.01 (0.21), residues: 656
  sheet: -0.95 (0.52), residues: 82
  loop : -1.53 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 213 
 TYR   0.014   0.001   TYR B 592 
 PHE   0.014   0.001   PHE B 284 
 TRP   0.004   0.001   TRP B 583 
 HIS   0.011   0.001   HIS B 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 8714)
  covalent geometry    : angle       0.57636 (11778)
  SS BOND              : bond        0.00190 (    2)
  SS BOND              : angle       1.30558 (    4)
  hydrogen bonds       : bond        0.03128 (  470)
  hydrogen bonds       : angle       3.54855 ( 1368)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 116
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8767 (mmm) cc_final: 0.8544 (mmm)
REVERT: A  500 MET cc_start: 0.8224 (tmm) cc_final: 0.7606 (tmm)
REVERT: A  628 GLU cc_start: 0.8670 (tp30) cc_final: 0.8086 (tm-30)
REVERT: B  179 MET cc_start: 0.8845 (mmm) cc_final: 0.8602 (mmm)
REVERT: B  500 MET cc_start: 0.8230 (tmm) cc_final: 0.7597 (tmm)
REVERT: B  628 GLU cc_start: 0.8678 (tp30) cc_final: 0.8287 (tm-30)
  outliers start: 36
  outliers final: 31
  residues processed: 134
  average time/residue: 0.0758
  time to fit residues: 15.2137
Evaluate side-chains
  139 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 108
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  450 MET
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  572 VAL
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  617 CYS
Chi-restraints excluded: chain B residue  645 ILE
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 22 optimal weight:    0.4980
   chunk 26 optimal weight:    9.9990
   chunk 23 optimal weight:    0.6980
   chunk 102 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 88 optimal weight:    0.7980
   chunk 48 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   chunk 39 optimal weight:    8.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** B 442 ASN ** 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 = 0.3278 r_free = 0.3278 target = 0.093820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.077363 restraints weight = 16756.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.080269 restraints weight = 8577.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.082303 restraints weight = 5433.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.083649 restraints weight = 3911.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.084666 restraints weight = 3103.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8716  Z= 0.150
  Angle     :  0.567   7.828  11782  Z= 0.277
  Chirality :  0.040   0.157   1356
  Planarity :  0.003   0.042   1474
  Dihedral  :  3.819  21.090   1188
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.60 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.27), residues: 1078
  helix:  2.07 (0.21), residues: 656
  sheet: -0.96 (0.51), residues: 82
  loop : -1.47 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 213 
 TYR   0.012   0.001   TYR B 592 
 PHE   0.015   0.001   PHE B 284 
 TRP   0.005   0.001   TRP B 583 
 HIS   0.007   0.001   HIS B 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8714)
  covalent geometry    : angle       0.56619 (11778)
  SS BOND              : bond        0.00078 (    2)
  SS BOND              : angle       1.37308 (    4)
  hydrogen bonds       : bond        0.03085 (  470)
  hydrogen bonds       : angle       3.52531 ( 1368)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8813 (mmm) cc_final: 0.8573 (mmm)
REVERT: A  500 MET cc_start: 0.8242 (tmm) cc_final: 0.7599 (tmm)
REVERT: A  628 GLU cc_start: 0.8674 (tp30) cc_final: 0.8103 (tm-30)
REVERT: B  179 MET cc_start: 0.8889 (mmm) cc_final: 0.8619 (mmm)
REVERT: B  500 MET cc_start: 0.8236 (tmm) cc_final: 0.7580 (tmm)
REVERT: B  628 GLU cc_start: 0.8685 (tp30) cc_final: 0.8304 (tm-30)
  outliers start: 32
  outliers final: 28
  residues processed: 130
  average time/residue: 0.0714
  time to fit residues: 14.2137
Evaluate side-chains
  137 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  450 MET
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  617 CYS
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 80 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 103 optimal weight:   10.0000
   chunk 48 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
** B 442 ASN ** 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 = 0.3316 r_free = 0.3316 target = 0.096588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.080317 restraints weight = 16669.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.083268 restraints weight = 8425.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.085370 restraints weight = 5282.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.086782 restraints weight = 3759.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.087803 restraints weight = 2948.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8716  Z= 0.113
  Angle     :  0.570   8.389  11782  Z= 0.274
  Chirality :  0.041   0.240   1356
  Planarity :  0.003   0.042   1474
  Dihedral  :  3.757  20.481   1188
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.81 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.27), residues: 1078
  helix:  2.11 (0.21), residues: 656
  sheet: -0.90 (0.51), residues: 82
  loop : -1.38 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 213 
 TYR   0.012   0.001   TYR B 592 
 PHE   0.016   0.001   PHE B 284 
 TRP   0.006   0.001   TRP A 583 
 HIS   0.007   0.001   HIS B 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8714)
  covalent geometry    : angle       0.56983 (11778)
  SS BOND              : bond        0.00614 (    2)
  SS BOND              : angle       1.34136 (    4)
  hydrogen bonds       : bond        0.02989 (  470)
  hydrogen bonds       : angle       3.47881 ( 1368)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  178 MET cc_start: 0.9406 (mmm) cc_final: 0.9187 (mmm)
REVERT: A  500 MET cc_start: 0.8246 (tmm) cc_final: 0.7627 (tmm)
REVERT: A  628 GLU cc_start: 0.8610 (tp30) cc_final: 0.8103 (tm-30)
REVERT: B  179 MET cc_start: 0.8838 (mmm) cc_final: 0.8598 (mmm)
REVERT: B  442 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.8727 (t0)
REVERT: B  500 MET cc_start: 0.8246 (tmm) cc_final: 0.7623 (tmm)
REVERT: B  628 GLU cc_start: 0.8632 (tp30) cc_final: 0.8122 (tm-30)
  outliers start: 26
  outliers final: 24
  residues processed: 133
  average time/residue: 0.0713
  time to fit residues: 14.4797
Evaluate side-chains
  136 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  450 MET
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  442 ASN
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  617 CYS
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 105 optimal weight:    0.9990
   chunk 54 optimal weight:   10.0000
   chunk 88 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 442 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.093654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.076750 restraints weight = 16829.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.079866 restraints weight = 8214.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.082029 restraints weight = 5043.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.083490 restraints weight = 3558.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.084548 restraints weight = 2776.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8716  Z= 0.165
  Angle     :  0.613   8.835  11782  Z= 0.294
  Chirality :  0.043   0.301   1356
  Planarity :  0.003   0.042   1474
  Dihedral  :  3.823  20.911   1188
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.35 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.27), residues: 1078
  helix:  2.09 (0.21), residues: 656
  sheet: -0.87 (0.52), residues: 82
  loop : -1.37 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 414 
 TYR   0.012   0.001   TYR B 592 
 PHE   0.016   0.001   PHE B 501 
 TRP   0.005   0.001   TRP A 511 
 HIS   0.007   0.001   HIS B 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 8714)
  covalent geometry    : angle       0.61255 (11778)
  SS BOND              : bond        0.00132 (    2)
  SS BOND              : angle       1.34612 (    4)
  hydrogen bonds       : bond        0.03176 (  470)
  hydrogen bonds       : angle       3.58750 ( 1368)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  500 MET cc_start: 0.8242 (tmm) cc_final: 0.7623 (tmm)
REVERT: A  628 GLU cc_start: 0.8704 (tp30) cc_final: 0.8092 (tm-30)
REVERT: B  179 MET cc_start: 0.8894 (mmm) cc_final: 0.8612 (mmm)
REVERT: B  500 MET cc_start: 0.8257 (tmm) cc_final: 0.7668 (tmm)
REVERT: B  628 GLU cc_start: 0.8720 (tp30) cc_final: 0.8117 (tm-30)
  outliers start: 27
  outliers final: 27
  residues processed: 128
  average time/residue: 0.0689
  time to fit residues: 13.5583
Evaluate side-chains
  138 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  450 MET
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  617 CYS
Chi-restraints excluded: chain B residue  645 ILE
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 73 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 103 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0670
   chunk 48 optimal weight:    5.9990
   overall best weight:    1.1324

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.094850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.078310 restraints weight = 16650.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.081352 restraints weight = 8311.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.083471 restraints weight = 5156.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.084960 restraints weight = 3661.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.085885 restraints weight = 2847.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8716  Z= 0.125
  Angle     :  0.606  10.130  11782  Z= 0.286
  Chirality :  0.043   0.337   1356
  Planarity :  0.003   0.042   1474
  Dihedral  :  3.791  20.733   1188
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.78 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.27), residues: 1078
  helix:  2.11 (0.21), residues: 656
  sheet: -0.87 (0.52), residues: 82
  loop : -1.31 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 213 
 TYR   0.012   0.001   TYR B 592 
 PHE   0.019   0.001   PHE B 501 
 TRP   0.005   0.001   TRP B 480 
 HIS   0.007   0.001   HIS B 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8714)
  covalent geometry    : angle       0.60583 (11778)
  SS BOND              : bond        0.00096 (    2)
  SS BOND              : angle       1.26620 (    4)
  hydrogen bonds       : bond        0.03078 (  470)
  hydrogen bonds       : angle       3.55506 ( 1368)

===============================================================================
Job complete
usr+sys time: 1296.28 seconds
wall clock time: 23 minutes 13.19 seconds (1393.19 seconds total)