Starting phenix.real_space_refine
on Tue Jul 29 01:40:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x1t_38001/07_2025/8x1t_38001_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x1t_38001/07_2025/8x1t_38001.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x1t_38001/07_2025/8x1t_38001.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x1t_38001/07_2025/8x1t_38001.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x1t_38001/07_2025/8x1t_38001_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x1t_38001/07_2025/8x1t_38001_neut.cif"
  }
  resolution = 2.47
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.155
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    7120      2.51       5
     N    1775      2.21       5
     O    1920      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 130 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10857
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 702, 5427
          Classifications: {'peptide': 702}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 670}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 46
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 5420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 701, 5420
          Classifications: {'peptide': 701}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 669}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 18
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'SO4': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'SO4': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.07, per 1000 atoms: 0.65
  Number of scatterers: 10857
  At special positions: 0
  Unit cell: (98.792, 117.432, 102.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1920      8.00
     N    1775      7.00
     C    7120      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.54
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2626

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 4 sheets defined
      68.3% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 25
    Processing helix  chain 'A' and resid 34 through 43
      removed outlier: 3.863A  pdb=" N   CYS A  43 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 58
    Processing helix  chain 'A' and resid 59 through 64
    Processing helix  chain 'A' and resid 68 through 99
      removed outlier: 6.171A  pdb=" N   LEU A  74 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 5.741A  pdb=" N   SER A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LEU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 120
      removed outlier: 3.687A  pdb=" N   LEU A 106 " --> pdb=" O   PRO A 102 " (cutoff:3.500A)
      Proline residue:  A 112  - end of helix
      removed outlier: 3.905A  pdb=" N   PHE A 118 " --> pdb=" O   ILE A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 148
    Processing helix  chain 'A' and resid 169 through 196
    Processing helix  chain 'A' and resid 200 through 205
    Processing helix  chain 'A' and resid 206 through 225
    Processing helix  chain 'A' and resid 225 through 230
    Processing helix  chain 'A' and resid 241 through 253
      removed outlier: 3.759A  pdb=" N   GLN A 253 " --> pdb=" O   SER A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 282
    Processing helix  chain 'A' and resid 291 through 307
      removed outlier: 3.514A  pdb=" N   ILE A 295 " --> pdb=" O   PRO A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 313
    Processing helix  chain 'A' and resid 332 through 339
    Processing helix  chain 'A' and resid 339 through 366
    Processing helix  chain 'A' and resid 370 through 388
    Processing helix  chain 'A' and resid 396 through 406
    Processing helix  chain 'A' and resid 411 through 427
    Processing helix  chain 'A' and resid 428 through 433
      removed outlier: 3.517A  pdb=" N   LEU A 431 " --> pdb=" O   ILE A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 453
      removed outlier: 3.855A  pdb=" N   LEU A 440 " --> pdb=" O   GLN A 436 " (cutoff:3.500A)
      removed outlier: 4.995A  pdb=" N   GLY A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   MET A 451 " --> pdb=" O   ASN A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 465
      removed outlier: 3.742A  pdb=" N   ARG A 460 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 482
    Processing helix  chain 'A' and resid 484 through 503
      removed outlier: 3.615A  pdb=" N   LEU A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE A 499 " --> pdb=" O   GLN A 495 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   VAL A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   THR A 503 " --> pdb=" O   ILE A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 561
    Processing helix  chain 'A' and resid 563 through 584
    Processing helix  chain 'A' and resid 612 through 618
      removed outlier: 3.586A  pdb=" N   VAL A 615 " --> pdb=" O   GLN A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 677
    Processing helix  chain 'A' and resid 687 through 697
    Processing helix  chain 'A' and resid 705 through 707
      No H-bonds generated for 'chain 'A' and resid 705 through 707'
    Processing helix  chain 'A' and resid 712 through 725
    Processing helix  chain 'B' and resid 17 through 25
    Processing helix  chain 'B' and resid 34 through 43
    Processing helix  chain 'B' and resid 46 through 58
    Processing helix  chain 'B' and resid 59 through 64
    Processing helix  chain 'B' and resid 68 through 99
      removed outlier: 5.936A  pdb=" N   LEU B  74 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   SER B  75 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU B  89 " --> pdb=" O   ILE B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 109
      removed outlier: 3.585A  pdb=" N   LEU B 106 " --> pdb=" O   PRO B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 120
      removed outlier: 3.537A  pdb=" N   ILE B 114 " --> pdb=" O   PHE B 110 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   PHE B 118 " --> pdb=" O   ILE B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 147
    Processing helix  chain 'B' and resid 170 through 196
    Processing helix  chain 'B' and resid 200 through 205
      removed outlier: 3.546A  pdb=" N   LEU B 205 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 225
    Processing helix  chain 'B' and resid 225 through 230
    Processing helix  chain 'B' and resid 241 through 253
    Processing helix  chain 'B' and resid 254 through 257
    Processing helix  chain 'B' and resid 258 through 282
    Processing helix  chain 'B' and resid 291 through 307
    Processing helix  chain 'B' and resid 308 through 313
    Processing helix  chain 'B' and resid 332 through 366
      removed outlier: 5.990A  pdb=" N   GLY B 341 " --> pdb=" O   GLN B 337 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   ASP B 342 " --> pdb=" O   ASN B 338 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   TYR B 361 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 388
    Processing helix  chain 'B' and resid 396 through 406
    Processing helix  chain 'B' and resid 411 through 427
    Processing helix  chain 'B' and resid 428 through 433
    Processing helix  chain 'B' and resid 436 through 447
      removed outlier: 3.642A  pdb=" N   LEU B 440 " --> pdb=" O   GLN B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 453
    Processing helix  chain 'B' and resid 456 through 465
      removed outlier: 3.637A  pdb=" N   ARG B 460 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 483
    Processing helix  chain 'B' and resid 483 through 504
      removed outlier: 3.546A  pdb=" N   ALA B 489 " --> pdb=" O   GLY B 485 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE B 499 " --> pdb=" O   GLN B 495 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL B 500 " --> pdb=" O   LEU B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 548 through 561
    Processing helix  chain 'B' and resid 563 through 585
    Processing helix  chain 'B' and resid 612 through 618
      removed outlier: 3.571A  pdb=" N   GLN B 618 " --> pdb=" O   VAL B 615 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 635 through 639
      removed outlier: 3.886A  pdb=" N   ASN B 638 " --> pdb=" O   LEU B 635 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 677
      removed outlier: 3.552A  pdb=" N   ILE B 677 " --> pdb=" O   GLU B 673 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 697
      removed outlier: 3.584A  pdb=" N   ILE B 691 " --> pdb=" O   ASP B 687 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ARG B 696 " --> pdb=" O   GLU B 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 709
    Processing helix  chain 'B' and resid 712 through 725
    Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13
    Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522
      removed outlier: 4.666A  pdb=" N   ILE A 537 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
      removed outlier: 8.541A  pdb=" N   ASN A 513 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 12.533A  pdb=" N   VAL A 535 " --> pdb=" O   ASN A 513 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   LYS A 536 " --> pdb=" O   ILE A 650 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   ASP A 652 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   PHE A 538 " --> pdb=" O   ASP A 652 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   PHE A 710 " --> pdb=" O   VAL A 681 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   ILE A 683 " --> pdb=" O   PHE A 710 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 589
    Processing sheet with id=AA4, first strand: chain 'B' and resid 520 through 522
      removed outlier: 4.481A  pdb=" N   ILE B 537 " --> pdb=" O   LEU B 511 " (cutoff:3.500A)
      removed outlier: 8.760A  pdb=" N   ASN B 513 " --> pdb=" O   VAL B 535 " (cutoff:3.500A)
      removed outlier: 12.507A  pdb=" N   VAL B 535 " --> pdb=" O   ASN B 513 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   LYS B 536 " --> pdb=" O   ILE B 650 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   ASP B 652 " --> pdb=" O   LYS B 536 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   PHE B 538 " --> pdb=" O   ASP B 652 " (cutoff:3.500A)

    685 hydrogen bonds defined for protein.
    1983 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: 4.02

  Time building geometry restraints manager: 3.05 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1874
        1.32 -     1.45: 2841
        1.45 -     1.58: 6316
        1.58 -     1.70: 0
        1.70 -     1.83: 60
  Bond restraints: 11091
  Sorted by residual:
  bond pdb=" C   LEU A 448 "
       pdb=" N   LYS A 449 "
    ideal  model  delta    sigma   weight residual
    1.335  1.258  0.078 1.32e-02 5.74e+03 3.45e+01
  bond pdb=" C   PRO A 506 "
       pdb=" N   LYS A 507 "
    ideal  model  delta    sigma   weight residual
    1.334  1.269  0.065 1.25e-02 6.40e+03 2.71e+01
  bond pdb=" C   ARG A 399 "
       pdb=" N   SER A 400 "
    ideal  model  delta    sigma   weight residual
    1.335  1.267  0.069 1.34e-02 5.57e+03 2.62e+01
  bond pdb=" C   ILE A 419 "
       pdb=" N   ILE A 420 "
    ideal  model  delta    sigma   weight residual
    1.334  1.273  0.061 1.26e-02 6.30e+03 2.34e+01
  bond pdb=" C   ILE A 677 "
       pdb=" N   LYS A 678 "
    ideal  model  delta    sigma   weight residual
    1.333  1.400 -0.067 1.45e-02 4.76e+03 2.14e+01
  ... (remaining 11086 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 14484
        2.14 -     4.28: 524
        4.28 -     6.42: 54
        6.42 -     8.56: 8
        8.56 -    10.70: 4
  Bond angle restraints: 15074
  Sorted by residual:
  angle pdb=" N   SER A  17 "
        pdb=" CA  SER A  17 "
        pdb=" C   SER A  17 "
      ideal   model   delta    sigma   weight residual
     110.55   99.85   10.70 1.35e+00 5.49e-01 6.29e+01
  angle pdb=" N   SER B  17 "
        pdb=" CA  SER B  17 "
        pdb=" C   SER B  17 "
      ideal   model   delta    sigma   weight residual
     110.42  100.46    9.96 1.55e+00 4.16e-01 4.13e+01
  angle pdb=" N   SER A 362 "
        pdb=" CA  SER A 362 "
        pdb=" C   SER A 362 "
      ideal   model   delta    sigma   weight residual
     111.14  104.47    6.67 1.08e+00 8.57e-01 3.81e+01
  angle pdb=" N   TYR A  16 "
        pdb=" CA  TYR A  16 "
        pdb=" C   TYR A  16 "
      ideal   model   delta    sigma   weight residual
     108.76  118.94  -10.18 1.69e+00 3.50e-01 3.63e+01
  angle pdb=" N   SER B 542 "
        pdb=" CA  SER B 542 "
        pdb=" C   SER B 542 "
      ideal   model   delta    sigma   weight residual
     108.07  112.58   -4.51 8.90e-01 1.26e+00 2.57e+01
  ... (remaining 15069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.74: 6021
       16.74 -    33.49: 459
       33.49 -    50.23: 79
       50.23 -    66.97: 22
       66.97 -    83.71: 5
  Dihedral angle restraints: 6586
    sinusoidal: 2521
      harmonic: 4065
  Sorted by residual:
  dihedral pdb=" C   GLU B 673 "
           pdb=" N   GLU B 673 "
           pdb=" CA  GLU B 673 "
           pdb=" CB  GLU B 673 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.95   12.35     0      2.50e+00 1.60e-01 2.44e+01
  dihedral pdb=" N   GLU B 673 "
           pdb=" C   GLU B 673 "
           pdb=" CA  GLU B 673 "
           pdb=" CB  GLU B 673 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.67  -11.87     0      2.50e+00 1.60e-01 2.25e+01
  dihedral pdb=" C   VAL A 241 "
           pdb=" N   VAL A 241 "
           pdb=" CA  VAL A 241 "
           pdb=" CB  VAL A 241 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.52   11.52     0      2.50e+00 1.60e-01 2.12e+01
  ... (remaining 6583 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 1674
       0.099 -    0.197: 115
       0.197 -    0.296: 7
       0.296 -    0.395: 2
       0.395 -    0.493: 2
  Chirality restraints: 1800
  Sorted by residual:
  chirality pdb=" CA  GLU B 673 "
            pdb=" N   GLU B 673 "
            pdb=" C   GLU B 673 "
            pdb=" CB  GLU B 673 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.08e+00
  chirality pdb=" CA  ILE A 613 "
            pdb=" N   ILE A 613 "
            pdb=" C   ILE A 613 "
            pdb=" CB  ILE A 613 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.02    0.42 2.00e-01 2.50e+01 4.33e+00
  chirality pdb=" CA  VAL A 241 "
            pdb=" N   VAL A 241 "
            pdb=" C   VAL A 241 "
            pdb=" CB  VAL A 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.06    0.38 2.00e-01 2.50e+01 3.63e+00
  ... (remaining 1797 not shown)

  Planarity restraints: 1883
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 329 "   -0.015 2.00e-02 2.50e+03   2.99e-02 8.92e+00
        pdb=" C   ILE B 329 "    0.052 2.00e-02 2.50e+03
        pdb=" O   ILE B 329 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR B 330 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 608 "   -0.014 2.00e-02 2.50e+03   2.93e-02 8.56e+00
        pdb=" C   LEU A 608 "    0.051 2.00e-02 2.50e+03
        pdb=" O   LEU A 608 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASP A 609 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 691 "    0.013 2.00e-02 2.50e+03   2.67e-02 7.14e+00
        pdb=" C   ILE B 691 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   ILE B 691 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLU B 692 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1880 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1489
        2.74 -     3.28: 11127
        3.28 -     3.82: 18628
        3.82 -     4.36: 23285
        4.36 -     4.90: 38373
  Nonbonded interactions: 92902
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  76 "
            pdb=" OG1 THR A 410 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OH  TYR A 116 "
            pdb=" OE1 GLU A 374 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   GLU A 293 "
            pdb=" OG1 THR A 297 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" NE2 GLN A 504 "
            pdb=" OH  TYR B 204 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" OD1 ASP A 525 "
            pdb=" NH1 ARG B  30 "
     model   vdw
     2.305 3.120
  ... (remaining 92897 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 7 through 150 or (resid 168 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 170 through 725 or resid 801))
  selection = (chain 'B' and (resid 7 through 43 or (resid 44 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 45 through 725 or resid 801))
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     27.920
  Find NCS groups from input model:        0.520
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
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      :  0.007   0.078  11091  Z= 0.473
  Angle     :  0.903  10.704  15074  Z= 0.610
  Chirality :  0.056   0.493   1800
  Planarity :  0.005   0.042   1883
  Dihedral  : 12.542  83.714   3960
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  9.59 %
    Favored  : 89.05 %
  Cbeta Deviations :  0.23 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.20), residues: 1395
  helix: -0.53 (0.16), residues: 906
  sheet:  0.82 (0.78), residues: 34
  loop : -1.30 (0.27), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  63 
 HIS   0.005   0.001   HIS B 220 
 PHE   0.019   0.002   PHE B 355 
 TYR   0.022   0.002   TYR A   9 
 ARG   0.003   0.000   ARG A 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17298 (  685)
  hydrogen bonds       : angle       6.37328 ( 1983)
  covalent geometry    : bond        0.00719 (11091)
  covalent geometry    : angle       0.90269 (15074)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 199
  time to evaluate  : 1.410 
Fit side-chains
REVERT: A   10 ILE cc_start: 0.8641 (mt) cc_final: 0.8374 (mm)
REVERT: A   23 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6510 (mt-10)
REVERT: A   24 ASN cc_start: 0.7197 (m-40) cc_final: 0.6870 (m-40)
REVERT: A   55 LEU cc_start: 0.7435 (mt) cc_final: 0.7189 (mt)
REVERT: A   57 LEU cc_start: 0.7845 (mt) cc_final: 0.7474 (mm)
REVERT: A   70 LYS cc_start: 0.7582 (ttmm) cc_final: 0.7111 (mppt)
REVERT: A  172 GLU cc_start: 0.6618 (pt0) cc_final: 0.5507 (mt-10)
REVERT: A  173 ARG cc_start: 0.6229 (ttp80) cc_final: 0.5787 (mtm110)
REVERT: A  320 ASP cc_start: 0.7401 (m-30) cc_final: 0.7192 (m-30)
REVERT: A  332 ASP cc_start: 0.6435 (m-30) cc_final: 0.6135 (t0)
REVERT: A  337 GLN cc_start: 0.6859 (mt0) cc_final: 0.6461 (tt0)
REVERT: A  507 LYS cc_start: 0.7342 (mmtm) cc_final: 0.7003 (mptt)
REVERT: A  527 TYR cc_start: 0.8246 (m-80) cc_final: 0.8032 (m-80)
REVERT: A  533 GLU cc_start: 0.7332 (tp30) cc_final: 0.6832 (pp20)
REVERT: A  573 LYS cc_start: 0.6945 (tttt) cc_final: 0.6599 (ttmm)
REVERT: A  614 GLU cc_start: 0.7016 (pt0) cc_final: 0.6252 (pm20)
REVERT: A  621 ASN cc_start: 0.7947 (t0) cc_final: 0.7662 (t0)
REVERT: A  630 ASP cc_start: 0.7103 (t0) cc_final: 0.6714 (t70)
REVERT: A  689 ASP cc_start: 0.7214 (m-30) cc_final: 0.6994 (m-30)
REVERT: A  703 GLU cc_start: 0.7679 (tt0) cc_final: 0.7374 (tt0)
REVERT: B   58 PHE cc_start: 0.7463 (t80) cc_final: 0.7256 (t80)
REVERT: B   70 LYS cc_start: 0.7797 (tttt) cc_final: 0.7015 (mppt)
REVERT: B  172 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6075 (mm-30)
REVERT: B  293 GLU cc_start: 0.6569 (mt-10) cc_final: 0.6183 (mp0)
REVERT: B  405 SER cc_start: 0.8375 (t) cc_final: 0.8151 (p)
REVERT: B  464 LYS cc_start: 0.8000 (mttt) cc_final: 0.7738 (mttp)
REVERT: B  507 LYS cc_start: 0.7822 (mttt) cc_final: 0.7310 (mptt)
REVERT: B  533 GLU cc_start: 0.6731 (tt0) cc_final: 0.6440 (tm-30)
REVERT: B  611 ASN cc_start: 0.6412 (m110) cc_final: 0.6208 (m-40)
REVERT: B  621 ASN cc_start: 0.7987 (t0) cc_final: 0.7647 (t0)
REVERT: B  681 VAL cc_start: 0.7913 (t) cc_final: 0.7688 (m)
  outliers start: 16
  outliers final: 2
  residues processed: 213
  average time/residue: 1.6998
  time to fit residues: 389.4503
Evaluate side-chains
  118 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 2.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain B residue  598 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    0.3980
   chunk 106 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 56 optimal weight:    9.9990
   chunk 109 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 66 optimal weight:    0.5980
   chunk 81 optimal weight:    0.3980
   chunk 127 optimal weight:   10.0000
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN
A 322 ASN
A 326 GLN
A 337 GLN
A 338 ASN
A 454 GLN
A 504 GLN
A 584 GLN
A 714 HIS
B   8 GLN
B  19 ASN
B  48 GLN
B  90 GLN
B 190 GLN
B 311 ASN
B 326 GLN
B 382 ASN
B 436 GLN
B 454 GLN
B 495 GLN
B 582 GLN
B 584 GLN
B 611 ASN
B 672 GLN
B 714 HIS

Total number of N/Q/H flips: 25

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.157814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.118514 restraints weight = 9847.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 1.41
r_work: 0.3087 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11091  Z= 0.127
  Angle     :  0.514   5.667  15074  Z= 0.278
  Chirality :  0.042   0.152   1800
  Planarity :  0.004   0.051   1883
  Dihedral  :  4.247  25.538   1496
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 11.46 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.23), residues: 1395
  helix:  1.28 (0.17), residues: 904
  sheet:  2.15 (0.82), residues: 34
  loop : -0.60 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  63 
 HIS   0.005   0.001   HIS B 647 
 PHE   0.021   0.001   PHE B 130 
 TYR   0.018   0.002   TYR A   9 
 ARG   0.003   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04607 (  685)
  hydrogen bonds       : angle       4.43196 ( 1983)
  covalent geometry    : bond        0.00267 (11091)
  covalent geometry    : angle       0.51384 (15074)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 2.393 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7341 (mt-10)
REVERT: A   56 SER cc_start: 0.8054 (OUTLIER) cc_final: 0.7838 (p)
REVERT: A   57 LEU cc_start: 0.8548 (mt) cc_final: 0.8305 (mm)
REVERT: A   58 PHE cc_start: 0.7899 (t80) cc_final: 0.7418 (m-80)
REVERT: A   70 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7724 (ptpp)
REVERT: A  172 GLU cc_start: 0.7175 (pt0) cc_final: 0.6154 (mt-10)
REVERT: A  173 ARG cc_start: 0.7119 (ttp80) cc_final: 0.6634 (mtm110)
REVERT: A  269 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8286 (tt)
REVERT: A  332 ASP cc_start: 0.7550 (m-30) cc_final: 0.7229 (t70)
REVERT: A  337 GLN cc_start: 0.7847 (mt0) cc_final: 0.7335 (tt0)
REVERT: A  507 LYS cc_start: 0.8281 (mmtm) cc_final: 0.8015 (mptt)
REVERT: A  527 TYR cc_start: 0.8554 (m-80) cc_final: 0.8338 (m-80)
REVERT: A  533 GLU cc_start: 0.8377 (tp30) cc_final: 0.8116 (tm-30)
REVERT: A  573 LYS cc_start: 0.8304 (tttt) cc_final: 0.8026 (ttmm)
REVERT: A  614 GLU cc_start: 0.7625 (pt0) cc_final: 0.6920 (pm20)
REVERT: A  630 ASP cc_start: 0.7618 (t0) cc_final: 0.7338 (t70)
REVERT: B   52 ARG cc_start: 0.6223 (mtm110) cc_final: 0.5672 (ptm160)
REVERT: B   58 PHE cc_start: 0.8072 (t80) cc_final: 0.7610 (m-80)
REVERT: B   70 LYS cc_start: 0.8003 (tttt) cc_final: 0.7142 (mppt)
REVERT: B  253 GLN cc_start: 0.7703 (mt0) cc_final: 0.7220 (pt0)
REVERT: B  293 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6982 (mp0)
REVERT: B  464 LYS cc_start: 0.8703 (mttt) cc_final: 0.8494 (mttp)
REVERT: B  507 LYS cc_start: 0.8717 (mttt) cc_final: 0.8342 (mptt)
REVERT: B  533 GLU cc_start: 0.8403 (tt0) cc_final: 0.7944 (tm-30)
REVERT: B  598 VAL cc_start: 0.6649 (OUTLIER) cc_final: 0.6255 (m)
REVERT: B  621 ASN cc_start: 0.8379 (t0) cc_final: 0.8110 (t0)
  outliers start: 23
  outliers final: 6
  residues processed: 153
  average time/residue: 1.8120
  time to fit residues: 300.6963
Evaluate side-chains
  122 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   56 SER
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  453 MET
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  598 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 122 optimal weight:    0.5980
   chunk 97 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 88 optimal weight:    0.6980
   chunk 134 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   chunk 130 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 513 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.154400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.114310 restraints weight = 9934.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 1.42
r_work: 0.3007 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11091  Z= 0.120
  Angle     :  0.481   5.298  15074  Z= 0.261
  Chirality :  0.041   0.131   1800
  Planarity :  0.004   0.051   1883
  Dihedral  :  4.084  25.022   1494
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 11.54 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.23), residues: 1395
  helix:  1.77 (0.18), residues: 902
  sheet:  2.64 (0.80), residues: 34
  loop : -0.26 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  63 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.018   0.001   PHE A 130 
 TYR   0.022   0.002   TYR A   9 
 ARG   0.002   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04445 (  685)
  hydrogen bonds       : angle       4.24737 ( 1983)
  covalent geometry    : bond        0.00254 (11091)
  covalent geometry    : angle       0.48141 (15074)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7410 (mt-10)
REVERT: A   57 LEU cc_start: 0.8738 (mt) cc_final: 0.8460 (mm)
REVERT: A   58 PHE cc_start: 0.8091 (t80) cc_final: 0.7634 (m-80)
REVERT: A  172 GLU cc_start: 0.7240 (pt0) cc_final: 0.6287 (mt-10)
REVERT: A  173 ARG cc_start: 0.7273 (ttp80) cc_final: 0.6805 (mtm110)
REVERT: A  269 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8369 (tt)
REVERT: A  332 ASP cc_start: 0.7911 (m-30) cc_final: 0.7479 (t0)
REVERT: A  337 GLN cc_start: 0.7902 (mt0) cc_final: 0.7476 (tt0)
REVERT: A  451 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7353 (ttm)
REVERT: A  507 LYS cc_start: 0.8599 (mmtm) cc_final: 0.8294 (mptt)
REVERT: A  533 GLU cc_start: 0.8440 (tp30) cc_final: 0.8077 (tm-30)
REVERT: A  573 LYS cc_start: 0.8383 (tttt) cc_final: 0.8175 (ttmm)
REVERT: A  614 GLU cc_start: 0.7761 (pt0) cc_final: 0.7077 (pm20)
REVERT: A  630 ASP cc_start: 0.7705 (t0) cc_final: 0.7418 (t70)
REVERT: B   52 ARG cc_start: 0.6351 (mtm110) cc_final: 0.5727 (ptm160)
REVERT: B   56 SER cc_start: 0.8504 (t) cc_final: 0.8227 (p)
REVERT: B   58 PHE cc_start: 0.8195 (t80) cc_final: 0.7815 (m-80)
REVERT: B   70 LYS cc_start: 0.8108 (tttt) cc_final: 0.7265 (mppt)
REVERT: B  253 GLN cc_start: 0.7649 (mt0) cc_final: 0.7313 (pt0)
REVERT: B  293 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7116 (mp0)
REVERT: B  464 LYS cc_start: 0.8734 (mttt) cc_final: 0.8527 (mttp)
REVERT: B  507 LYS cc_start: 0.8748 (mttt) cc_final: 0.8444 (mptt)
REVERT: B  533 GLU cc_start: 0.8492 (tt0) cc_final: 0.8024 (tm-30)
REVERT: B  598 VAL cc_start: 0.6575 (OUTLIER) cc_final: 0.6173 (m)
REVERT: B  621 ASN cc_start: 0.8313 (t0) cc_final: 0.8090 (t0)
  outliers start: 18
  outliers final: 8
  residues processed: 132
  average time/residue: 1.4047
  time to fit residues: 198.9467
Evaluate side-chains
  129 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  451 MET
Chi-restraints excluded: chain A residue  453 MET
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain B residue  601 ILE
Chi-restraints excluded: chain B residue  615 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   chunk 30 optimal weight:   10.0000
   chunk 127 optimal weight:   30.0000
   chunk 54 optimal weight:    0.8980
   chunk 123 optimal weight:    0.0970
   chunk 99 optimal weight:    0.7980
   chunk 114 optimal weight:    0.7980
   overall best weight:    0.6378

-------------------------------------------------------------------------------
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 = 0.3733 r_free = 0.3733 target = 0.154444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.114439 restraints weight = 9748.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.42
r_work: 0.3029 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  11091  Z= 0.112
  Angle     :  0.465   5.194  15074  Z= 0.251
  Chirality :  0.041   0.132   1800
  Planarity :  0.004   0.054   1883
  Dihedral  :  4.030  24.814   1494
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 10.78 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.23), residues: 1395
  helix:  1.95 (0.18), residues: 904
  sheet:  2.91 (0.81), residues: 34
  loop : -0.19 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  63 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.017   0.001   PHE A 130 
 TYR   0.021   0.002   TYR A   9 
 ARG   0.008   0.000   ARG B 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04139 (  685)
  hydrogen bonds       : angle       4.14509 ( 1983)
  covalent geometry    : bond        0.00240 (11091)
  covalent geometry    : angle       0.46473 (15074)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.8661 (mt) cc_final: 0.8394 (mm)
REVERT: A   58 PHE cc_start: 0.8026 (t80) cc_final: 0.7590 (m-80)
REVERT: A  172 GLU cc_start: 0.7029 (pt0) cc_final: 0.6120 (mt-10)
REVERT: A  269 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8316 (tt)
REVERT: A  332 ASP cc_start: 0.7617 (m-30) cc_final: 0.7262 (t0)
REVERT: A  337 GLN cc_start: 0.7745 (mt0) cc_final: 0.7431 (pt0)
REVERT: A  451 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7176 (ttm)
REVERT: A  507 LYS cc_start: 0.8538 (mmtm) cc_final: 0.8262 (mmtm)
REVERT: A  533 GLU cc_start: 0.8295 (tp30) cc_final: 0.7976 (tm-30)
REVERT: A  573 LYS cc_start: 0.8304 (tttt) cc_final: 0.8047 (ttmm)
REVERT: A  614 GLU cc_start: 0.7669 (pt0) cc_final: 0.6968 (pm20)
REVERT: A  630 ASP cc_start: 0.7724 (t0) cc_final: 0.7436 (t70)
REVERT: B   52 ARG cc_start: 0.6282 (mtm110) cc_final: 0.5658 (ptm160)
REVERT: B   56 SER cc_start: 0.8266 (t) cc_final: 0.7988 (p)
REVERT: B   58 PHE cc_start: 0.8064 (t80) cc_final: 0.7707 (m-80)
REVERT: B   70 LYS cc_start: 0.8231 (tttt) cc_final: 0.7278 (mppt)
REVERT: B  253 GLN cc_start: 0.7384 (mt0) cc_final: 0.7027 (pt0)
REVERT: B  269 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8281 (tt)
REVERT: B  293 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7162 (mp0)
REVERT: B  464 LYS cc_start: 0.8694 (mttt) cc_final: 0.8452 (mtpt)
REVERT: B  507 LYS cc_start: 0.8727 (mttt) cc_final: 0.8112 (tttm)
REVERT: B  533 GLU cc_start: 0.8449 (tt0) cc_final: 0.7936 (tm-30)
REVERT: B  612 GLN cc_start: 0.7044 (mt0) cc_final: 0.6774 (mt0)
REVERT: B  621 ASN cc_start: 0.8200 (t0) cc_final: 0.7956 (t0)
  outliers start: 24
  outliers final: 12
  residues processed: 145
  average time/residue: 1.3733
  time to fit residues: 213.8440
Evaluate side-chains
  136 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  451 MET
Chi-restraints excluded: chain A residue  453 MET
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain B residue  601 ILE
Chi-restraints excluded: chain B residue  615 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 133 optimal weight:    4.9990
   chunk 108 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 126 optimal weight:   10.0000
   chunk 107 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 78 optimal weight:    4.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
B   7 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.150208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.109474 restraints weight = 9627.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.43
r_work: 0.2956 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  11091  Z= 0.193
  Angle     :  0.554   6.093  15074  Z= 0.301
  Chirality :  0.045   0.220   1800
  Planarity :  0.005   0.060   1883
  Dihedral  :  4.389  25.713   1494
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 10.78 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.23), residues: 1395
  helix:  1.72 (0.17), residues: 904
  sheet:  2.96 (0.81), residues: 34
  loop : -0.21 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  63 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.019   0.002   PHE A 130 
 TYR   0.027   0.002   TYR B   9 
 ARG   0.010   0.001   ARG B 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05366 (  685)
  hydrogen bonds       : angle       4.42449 ( 1983)
  covalent geometry    : bond        0.00460 (11091)
  covalent geometry    : angle       0.55369 (15074)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7370 (mt-10)
REVERT: A   52 ARG cc_start: 0.6704 (ptt90) cc_final: 0.6246 (ttp-110)
REVERT: A   57 LEU cc_start: 0.8740 (mt) cc_final: 0.8428 (mm)
REVERT: A   58 PHE cc_start: 0.8131 (t80) cc_final: 0.7729 (m-80)
REVERT: A  172 GLU cc_start: 0.7084 (pt0) cc_final: 0.6209 (mt-10)
REVERT: A  269 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8343 (tt)
REVERT: A  332 ASP cc_start: 0.7673 (m-30) cc_final: 0.7318 (t0)
REVERT: A  337 GLN cc_start: 0.7906 (mt0) cc_final: 0.7463 (tt0)
REVERT: A  507 LYS cc_start: 0.8584 (mmtm) cc_final: 0.8301 (mmtm)
REVERT: A  533 GLU cc_start: 0.8311 (tp30) cc_final: 0.7960 (tm-30)
REVERT: A  573 LYS cc_start: 0.8298 (tttt) cc_final: 0.8035 (ttmm)
REVERT: A  614 GLU cc_start: 0.7673 (pt0) cc_final: 0.6952 (pm20)
REVERT: A  621 ASN cc_start: 0.8435 (t0) cc_final: 0.8099 (t0)
REVERT: A  630 ASP cc_start: 0.7681 (t0) cc_final: 0.7417 (t70)
REVERT: B   56 SER cc_start: 0.8333 (t) cc_final: 0.8093 (p)
REVERT: B   58 PHE cc_start: 0.8082 (t80) cc_final: 0.7709 (m-80)
REVERT: B   70 LYS cc_start: 0.8292 (tttt) cc_final: 0.7356 (mppt)
REVERT: B  269 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8327 (tt)
REVERT: B  293 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7267 (mp0)
REVERT: B  464 LYS cc_start: 0.8739 (mttt) cc_final: 0.8485 (mtpt)
REVERT: B  507 LYS cc_start: 0.8709 (mttt) cc_final: 0.8091 (tttm)
REVERT: B  533 GLU cc_start: 0.8517 (tt0) cc_final: 0.8057 (pp20)
REVERT: B  612 GLN cc_start: 0.7247 (mt0) cc_final: 0.6958 (mt0)
REVERT: B  621 ASN cc_start: 0.8249 (t0) cc_final: 0.7988 (t0)
  outliers start: 30
  outliers final: 15
  residues processed: 146
  average time/residue: 1.4044
  time to fit residues: 219.6279
Evaluate side-chains
  143 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 1.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  453 MET
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  607 GLU
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain B residue  601 ILE
Chi-restraints excluded: chain B residue  615 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 135 optimal weight:    3.9990
   chunk 119 optimal weight:    0.6980
   chunk 101 optimal weight:    0.4980
   chunk 45 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 113 optimal weight:    5.9990
   chunk 60 optimal weight:    0.0770
   chunk 8 optimal weight:    4.9990
   chunk 122 optimal weight:    0.4980
   chunk 130 optimal weight:    1.9990
   overall best weight:    0.7540

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.152574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.112315 restraints weight = 9821.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 1.41
r_work: 0.2999 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2885 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.2978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11091  Z= 0.120
  Angle     :  0.479   5.222  15074  Z= 0.260
  Chirality :  0.041   0.157   1800
  Planarity :  0.004   0.057   1883
  Dihedral  :  4.162  25.697   1494
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.71 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.23), residues: 1395
  helix:  1.95 (0.18), residues: 901
  sheet:  3.05 (0.84), residues: 34
  loop : -0.14 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  63 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.018   0.001   PHE A 130 
 TYR   0.022   0.002   TYR A   9 
 ARG   0.010   0.000   ARG B 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04361 (  685)
  hydrogen bonds       : angle       4.22244 ( 1983)
  covalent geometry    : bond        0.00263 (11091)
  covalent geometry    : angle       0.47854 (15074)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 1.197 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.8700 (mt) cc_final: 0.8392 (mm)
REVERT: A   58 PHE cc_start: 0.8050 (t80) cc_final: 0.7682 (m-80)
REVERT: A  172 GLU cc_start: 0.7081 (pt0) cc_final: 0.6232 (mt-10)
REVERT: A  269 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8337 (tt)
REVERT: A  332 ASP cc_start: 0.7610 (m-30) cc_final: 0.7284 (t0)
REVERT: A  337 GLN cc_start: 0.7792 (mt0) cc_final: 0.7472 (pt0)
REVERT: A  507 LYS cc_start: 0.8611 (mmtm) cc_final: 0.8351 (mmtm)
REVERT: A  533 GLU cc_start: 0.8263 (tp30) cc_final: 0.7925 (tm-30)
REVERT: A  573 LYS cc_start: 0.8236 (tttt) cc_final: 0.8015 (ttmm)
REVERT: A  630 ASP cc_start: 0.7675 (t0) cc_final: 0.7412 (t70)
REVERT: A  643 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8221 (mmtp)
REVERT: B   58 PHE cc_start: 0.8014 (t80) cc_final: 0.7612 (m-80)
REVERT: B   70 LYS cc_start: 0.8299 (tttt) cc_final: 0.7350 (mppt)
REVERT: B  269 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8291 (tt)
REVERT: B  293 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7236 (mp0)
REVERT: B  464 LYS cc_start: 0.8687 (mttt) cc_final: 0.8462 (mtpt)
REVERT: B  507 LYS cc_start: 0.8718 (mttt) cc_final: 0.8104 (tttm)
REVERT: B  533 GLU cc_start: 0.8470 (tt0) cc_final: 0.8020 (pp20)
REVERT: B  609 ASP cc_start: 0.7875 (p0) cc_final: 0.7608 (p0)
REVERT: B  612 GLN cc_start: 0.7240 (mt0) cc_final: 0.6967 (mt0)
REVERT: B  621 ASN cc_start: 0.8245 (t0) cc_final: 0.7989 (t0)
  outliers start: 24
  outliers final: 13
  residues processed: 140
  average time/residue: 1.4180
  time to fit residues: 212.8564
Evaluate side-chains
  138 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  453 MET
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  607 GLU
Chi-restraints excluded: chain A residue  643 LYS
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  601 ILE
Chi-restraints excluded: chain B residue  615 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 135 optimal weight:    3.9990
   chunk 136 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 128 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 124 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 672 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.150320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.109425 restraints weight = 9917.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.43
r_work: 0.2957 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  11091  Z= 0.176
  Angle     :  0.534   5.942  15074  Z= 0.291
  Chirality :  0.044   0.210   1800
  Planarity :  0.005   0.059   1883
  Dihedral  :  4.343  25.791   1493
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.29 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.23), residues: 1395
  helix:  1.76 (0.17), residues: 902
  sheet:  2.98 (0.83), residues: 34
  loop : -0.20 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  63 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.018   0.002   PHE B 130 
 TYR   0.026   0.002   TYR B   9 
 ARG   0.012   0.001   ARG B 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05143 (  685)
  hydrogen bonds       : angle       4.37362 ( 1983)
  covalent geometry    : bond        0.00418 (11091)
  covalent geometry    : angle       0.53375 (15074)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 1.165 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.8748 (mt) cc_final: 0.8411 (mm)
REVERT: A   58 PHE cc_start: 0.8107 (t80) cc_final: 0.7734 (m-80)
REVERT: A  172 GLU cc_start: 0.7182 (pt0) cc_final: 0.6370 (mt-10)
REVERT: A  269 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8357 (tt)
REVERT: A  332 ASP cc_start: 0.7629 (m-30) cc_final: 0.7328 (t0)
REVERT: A  337 GLN cc_start: 0.7875 (mt0) cc_final: 0.7461 (tt0)
REVERT: A  507 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8413 (mmtm)
REVERT: A  533 GLU cc_start: 0.8261 (tp30) cc_final: 0.7937 (tm-30)
REVERT: A  573 LYS cc_start: 0.8299 (tttt) cc_final: 0.8042 (ttmm)
REVERT: A  621 ASN cc_start: 0.8389 (t0) cc_final: 0.8090 (t0)
REVERT: A  630 ASP cc_start: 0.7688 (t0) cc_final: 0.7429 (t70)
REVERT: A  643 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8275 (mmtp)
REVERT: B   58 PHE cc_start: 0.8089 (t80) cc_final: 0.7694 (m-80)
REVERT: B   70 LYS cc_start: 0.8312 (tttt) cc_final: 0.7354 (mppt)
REVERT: B  269 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8316 (tt)
REVERT: B  293 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7334 (mp0)
REVERT: B  464 LYS cc_start: 0.8729 (mttt) cc_final: 0.8494 (mtpt)
REVERT: B  507 LYS cc_start: 0.8690 (mttt) cc_final: 0.8085 (tttm)
REVERT: B  533 GLU cc_start: 0.8490 (tt0) cc_final: 0.8045 (pp20)
REVERT: B  609 ASP cc_start: 0.7910 (p0) cc_final: 0.7686 (p0)
REVERT: B  612 GLN cc_start: 0.7255 (mt0) cc_final: 0.7008 (mt0)
REVERT: B  621 ASN cc_start: 0.8302 (t0) cc_final: 0.8047 (t0)
  outliers start: 24
  outliers final: 16
  residues processed: 141
  average time/residue: 1.3091
  time to fit residues: 198.2118
Evaluate side-chains
  143 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 1.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  453 MET
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  607 GLU
Chi-restraints excluded: chain A residue  643 LYS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  601 ILE
Chi-restraints excluded: chain B residue  615 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 81 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 77 optimal weight:    6.9990
   chunk 87 optimal weight:    0.6980
   chunk 3 optimal weight:   20.0000
   chunk 79 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 135 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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 = 0.3687 r_free = 0.3687 target = 0.150381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.109826 restraints weight = 9736.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 1.41
r_work: 0.2966 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  11091  Z= 0.168
  Angle     :  0.530   5.943  15074  Z= 0.289
  Chirality :  0.044   0.210   1800
  Planarity :  0.005   0.060   1883
  Dihedral  :  4.366  25.810   1493
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.29 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.23), residues: 1395
  helix:  1.75 (0.17), residues: 902
  sheet:  2.96 (0.84), residues: 34
  loop : -0.16 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  63 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.018   0.002   PHE B 130 
 TYR   0.025   0.002   TYR B   9 
 ARG   0.013   0.001   ARG B 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05077 (  685)
  hydrogen bonds       : angle       4.37173 ( 1983)
  covalent geometry    : bond        0.00397 (11091)
  covalent geometry    : angle       0.53017 (15074)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 1.222 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.8718 (mt) cc_final: 0.8375 (mm)
REVERT: A   58 PHE cc_start: 0.8098 (t80) cc_final: 0.7738 (m-80)
REVERT: A  172 GLU cc_start: 0.7132 (pt0) cc_final: 0.6380 (mt-10)
REVERT: A  269 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8345 (tt)
REVERT: A  332 ASP cc_start: 0.7383 (m-30) cc_final: 0.7123 (t0)
REVERT: A  337 GLN cc_start: 0.7860 (mt0) cc_final: 0.7448 (tt0)
REVERT: A  507 LYS cc_start: 0.8670 (mmtm) cc_final: 0.8412 (mmtm)
REVERT: A  533 GLU cc_start: 0.8231 (tp30) cc_final: 0.7917 (pp20)
REVERT: A  573 LYS cc_start: 0.8279 (tttt) cc_final: 0.8010 (ttmm)
REVERT: A  612 GLN cc_start: 0.7228 (mt0) cc_final: 0.7013 (mt0)
REVERT: A  621 ASN cc_start: 0.8371 (t0) cc_final: 0.8079 (t0)
REVERT: A  630 ASP cc_start: 0.7679 (t0) cc_final: 0.7419 (t70)
REVERT: A  643 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8256 (mmtp)
REVERT: B   58 PHE cc_start: 0.8081 (t80) cc_final: 0.7671 (m-80)
REVERT: B   70 LYS cc_start: 0.8344 (tttt) cc_final: 0.7354 (mppt)
REVERT: B  253 GLN cc_start: 0.7748 (mt0) cc_final: 0.7503 (pt0)
REVERT: B  269 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8299 (tt)
REVERT: B  293 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7171 (mp0)
REVERT: B  296 MET cc_start: 0.8375 (mmm) cc_final: 0.8172 (mmp)
REVERT: B  464 LYS cc_start: 0.8713 (mttt) cc_final: 0.8475 (mtpt)
REVERT: B  507 LYS cc_start: 0.8700 (mttt) cc_final: 0.8099 (tttm)
REVERT: B  533 GLU cc_start: 0.8506 (tt0) cc_final: 0.8054 (pp20)
REVERT: B  609 ASP cc_start: 0.7901 (p0) cc_final: 0.7667 (p0)
REVERT: B  612 GLN cc_start: 0.7246 (mt0) cc_final: 0.7015 (mt0)
REVERT: B  621 ASN cc_start: 0.8304 (t0) cc_final: 0.8042 (t0)
  outliers start: 24
  outliers final: 18
  residues processed: 143
  average time/residue: 1.3293
  time to fit residues: 204.5109
Evaluate side-chains
  147 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 1.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  453 MET
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  607 GLU
Chi-restraints excluded: chain A residue  643 LYS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  453 MET
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain B residue  601 ILE
Chi-restraints excluded: chain B residue  615 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 73 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 130 optimal weight:    3.9990
   chunk 136 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 29 optimal weight:    0.4980
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3692 r_free = 0.3692 target = 0.150803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.110328 restraints weight = 9805.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.41
r_work: 0.2974 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  11091  Z= 0.151
  Angle     :  0.512   5.696  15074  Z= 0.279
  Chirality :  0.043   0.210   1800
  Planarity :  0.004   0.060   1883
  Dihedral  :  4.305  25.727   1493
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.12 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.23), residues: 1395
  helix:  1.85 (0.17), residues: 902
  sheet:  2.97 (0.84), residues: 34
  loop : -0.10 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  63 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.018   0.001   PHE B 130 
 TYR   0.024   0.002   TYR B   9 
 ARG   0.014   0.000   ARG B 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04849 (  685)
  hydrogen bonds       : angle       4.32423 ( 1983)
  covalent geometry    : bond        0.00350 (11091)
  covalent geometry    : angle       0.51240 (15074)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 1.296 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.8714 (mt) cc_final: 0.8375 (mm)
REVERT: A   58 PHE cc_start: 0.8082 (t80) cc_final: 0.7706 (m-80)
REVERT: A   99 ASP cc_start: 0.8569 (t0) cc_final: 0.8331 (t70)
REVERT: A  172 GLU cc_start: 0.7077 (pt0) cc_final: 0.6358 (mt-10)
REVERT: A  174 VAL cc_start: 0.8495 (t) cc_final: 0.8155 (p)
REVERT: A  269 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8340 (tt)
REVERT: A  332 ASP cc_start: 0.7283 (m-30) cc_final: 0.7036 (t0)
REVERT: A  337 GLN cc_start: 0.7860 (mt0) cc_final: 0.7473 (pt0)
REVERT: A  451 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7342 (ttm)
REVERT: A  507 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8374 (mmtm)
REVERT: A  533 GLU cc_start: 0.8248 (tp30) cc_final: 0.7962 (pp20)
REVERT: A  573 LYS cc_start: 0.8302 (tttt) cc_final: 0.8045 (ttmm)
REVERT: A  621 ASN cc_start: 0.8371 (t0) cc_final: 0.8083 (t0)
REVERT: A  630 ASP cc_start: 0.7707 (t0) cc_final: 0.7460 (t70)
REVERT: A  643 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8260 (mmtp)
REVERT: B   58 PHE cc_start: 0.8072 (t80) cc_final: 0.7668 (m-80)
REVERT: B   70 LYS cc_start: 0.8334 (tttt) cc_final: 0.7355 (mppt)
REVERT: B  253 GLN cc_start: 0.7673 (mt0) cc_final: 0.7376 (pt0)
REVERT: B  269 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8314 (tt)
REVERT: B  293 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7151 (mp0)
REVERT: B  464 LYS cc_start: 0.8706 (mttt) cc_final: 0.8476 (mtpt)
REVERT: B  507 LYS cc_start: 0.8691 (mttt) cc_final: 0.8100 (tttm)
REVERT: B  533 GLU cc_start: 0.8494 (tt0) cc_final: 0.8049 (pp20)
REVERT: B  609 ASP cc_start: 0.7907 (p0) cc_final: 0.7613 (p0)
REVERT: B  612 GLN cc_start: 0.7262 (mt0) cc_final: 0.6967 (mt0)
REVERT: B  621 ASN cc_start: 0.8309 (t0) cc_final: 0.8038 (t0)
  outliers start: 26
  outliers final: 17
  residues processed: 137
  average time/residue: 1.3513
  time to fit residues: 198.9751
Evaluate side-chains
  144 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  451 MET
Chi-restraints excluded: chain A residue  453 MET
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  607 GLU
Chi-restraints excluded: chain A residue  643 LYS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  453 MET
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  601 ILE
Chi-restraints excluded: chain B residue  615 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 86 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 4 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 110 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 125 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 103 optimal weight:    4.9990
   chunk 75 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3689 r_free = 0.3689 target = 0.150547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.110111 restraints weight = 9739.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.41
r_work: 0.2970 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  11091  Z= 0.156
  Angle     :  0.524   5.893  15074  Z= 0.285
  Chirality :  0.043   0.225   1800
  Planarity :  0.005   0.060   1883
  Dihedral  :  4.334  25.697   1493
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.71 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.23), residues: 1395
  helix:  1.82 (0.17), residues: 902
  sheet:  2.95 (0.84), residues: 34
  loop : -0.09 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  63 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.018   0.002   PHE B 130 
 TYR   0.024   0.002   TYR B   9 
 ARG   0.014   0.000   ARG B 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04936 (  685)
  hydrogen bonds       : angle       4.34792 ( 1983)
  covalent geometry    : bond        0.00364 (11091)
  covalent geometry    : angle       0.52421 (15074)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 1.207 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.8706 (mt) cc_final: 0.8365 (mm)
REVERT: A   58 PHE cc_start: 0.8075 (t80) cc_final: 0.7704 (m-80)
REVERT: A   99 ASP cc_start: 0.8596 (t0) cc_final: 0.8358 (t70)
REVERT: A  172 GLU cc_start: 0.7030 (pt0) cc_final: 0.6333 (mt-10)
REVERT: A  174 VAL cc_start: 0.8463 (t) cc_final: 0.8123 (p)
REVERT: A  269 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8340 (tt)
REVERT: A  332 ASP cc_start: 0.7262 (m-30) cc_final: 0.7020 (t0)
REVERT: A  337 GLN cc_start: 0.7843 (mt0) cc_final: 0.7453 (pt0)
REVERT: A  451 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7352 (ttm)
REVERT: A  507 LYS cc_start: 0.8652 (mmtm) cc_final: 0.8391 (mmtm)
REVERT: A  533 GLU cc_start: 0.8211 (tp30) cc_final: 0.7945 (pp20)
REVERT: A  573 LYS cc_start: 0.8285 (tttt) cc_final: 0.8019 (ttmm)
REVERT: A  612 GLN cc_start: 0.7210 (mt0) cc_final: 0.7005 (mt0)
REVERT: A  621 ASN cc_start: 0.8356 (t0) cc_final: 0.8088 (t0)
REVERT: A  630 ASP cc_start: 0.7691 (t0) cc_final: 0.7431 (t70)
REVERT: A  643 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8250 (mmtp)
REVERT: B   58 PHE cc_start: 0.8084 (t80) cc_final: 0.7677 (m-80)
REVERT: B   70 LYS cc_start: 0.8343 (tttt) cc_final: 0.7346 (mppt)
REVERT: B  269 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8302 (tt)
REVERT: B  293 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7160 (mp0)
REVERT: B  464 LYS cc_start: 0.8710 (mttt) cc_final: 0.8479 (mtpt)
REVERT: B  507 LYS cc_start: 0.8693 (mttt) cc_final: 0.8095 (tttm)
REVERT: B  533 GLU cc_start: 0.8488 (tt0) cc_final: 0.8039 (pp20)
REVERT: B  609 ASP cc_start: 0.7883 (p0) cc_final: 0.7609 (p0)
REVERT: B  612 GLN cc_start: 0.7255 (mt0) cc_final: 0.6972 (mt0)
REVERT: B  621 ASN cc_start: 0.8292 (t0) cc_final: 0.8016 (t0)
  outliers start: 24
  outliers final: 18
  residues processed: 138
  average time/residue: 1.3785
  time to fit residues: 204.5645
Evaluate side-chains
  146 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  451 MET
Chi-restraints excluded: chain A residue  453 MET
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  607 GLU
Chi-restraints excluded: chain A residue  643 LYS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  453 MET
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain B residue  601 ILE
Chi-restraints excluded: chain B residue  615 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 130 optimal weight:    0.7980
   chunk 137 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 126 optimal weight:    0.9990
   chunk 134 optimal weight:    0.5980
   chunk 133 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 94 optimal weight:    5.9990
   chunk 57 optimal weight:   20.0000
   chunk 61 optimal weight:    0.0030
   overall best weight:    0.5990

-------------------------------------------------------------------------------
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 = 0.3717 r_free = 0.3717 target = 0.152988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.112974 restraints weight = 9787.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.42
r_work: 0.3011 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  11091  Z= 0.111
  Angle     :  0.469   5.249  15074  Z= 0.255
  Chirality :  0.041   0.193   1800
  Planarity :  0.004   0.060   1883
  Dihedral  :  4.099  25.360   1493
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.97 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.23), residues: 1395
  helix:  2.03 (0.17), residues: 903
  sheet:  3.08 (0.85), residues: 34
  loop : -0.02 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  63 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.017   0.001   PHE A 130 
 TYR   0.020   0.001   TYR B   9 
 ARG   0.014   0.000   ARG B 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04149 (  685)
  hydrogen bonds       : angle       4.17807 ( 1983)
  covalent geometry    : bond        0.00236 (11091)
  covalent geometry    : angle       0.46890 (15074)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9574.21 seconds
wall clock time: 168 minutes 40.79 seconds (10120.79 seconds total)