Starting phenix.real_space_refine
on Mon Jun  9 04:05:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lh3_23335/06_2025/7lh3_23335.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lh3_23335/06_2025/7lh3_23335.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lh3_23335/06_2025/7lh3_23335.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lh3_23335/06_2025/7lh3_23335.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lh3_23335/06_2025/7lh3_23335.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lh3_23335/06_2025/7lh3_23335.cif"
  }
  resolution = 4.3
  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=   0.007 sd=   0.020
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      48      5.16       5
     C    6862      2.51       5
     N    1690      2.21       5
     O    1852      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10452
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 680, 5226
          Classifications: {'peptide': 680}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 34, 'TRANS': 645}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 29
  Restraints were copied for chains:
    B
  Time building chain proxies: 10.28, per 1000 atoms: 0.98
  Number of scatterers: 10452
  At special positions: 0
  Unit cell: (102.16, 119.078, 113.222, 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      48     16.00
     O    1852      8.00
     N    1690      7.00
     C    6862      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: 2.92
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2512

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 5 sheets defined
      71.5% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 31
    Processing helix  chain 'A' and resid 41 through 48
      removed outlier: 4.243A  pdb=" N   GLN A  48 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 51
      No H-bonds generated for 'chain 'A' and resid 49 through 51'
    Processing helix  chain 'A' and resid 53 through 65
    Processing helix  chain 'A' and resid 66 through 71
    Processing helix  chain 'A' and resid 75 through 105
      removed outlier: 5.182A  pdb=" N   LEU A  81 " --> pdb=" O   LYS A  77 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   GLY A  82 " --> pdb=" O   GLU A  78 " (cutoff:3.500A)
      Proline residue:  A  96  - end of helix
    Processing helix  chain 'A' and resid 108 through 115
      removed outlier: 3.988A  pdb=" N   GLY A 112 " --> pdb=" O   PRO A 108 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU A 113 " --> pdb=" O   PRO A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 127
      removed outlier: 3.715A  pdb=" N   PHE A 125 " --> pdb=" O   ILE A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 152
    Processing helix  chain 'A' and resid 168 through 196
    Processing helix  chain 'A' and resid 197 through 205
      removed outlier: 4.087A  pdb=" N   PHE A 200 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE A 203 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 225
    Processing helix  chain 'A' and resid 225 through 231
    Processing helix  chain 'A' and resid 241 through 253
    Processing helix  chain 'A' and resid 254 through 257
    Processing helix  chain 'A' and resid 258 through 282
    Processing helix  chain 'A' and resid 291 through 308
      removed outlier: 3.543A  pdb=" N   PHE A 295 " --> pdb=" O   PRO A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 313
      removed outlier: 3.744A  pdb=" N   TYR A 313 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 366
      removed outlier: 6.430A  pdb=" N   VAL A 341 " --> pdb=" O   HIS A 337 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   ASP A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    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 428
      removed outlier: 3.513A  pdb=" N   CYS A 415 " --> pdb=" O   GLN A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 435
      removed outlier: 4.188A  pdb=" N   SER A 434 " --> pdb=" O   LEU A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 448
      removed outlier: 3.847A  pdb=" N   LEU A 440 " --> pdb=" O   PRO A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 453
    Processing helix  chain 'A' and resid 456 through 465
      removed outlier: 3.875A  pdb=" N   PHE A 460 " --> pdb=" O   SER A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 481
    Processing helix  chain 'A' and resid 483 through 505
      removed outlier: 3.713A  pdb=" N   LEU A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   ILE A 489 " --> pdb=" O   ASP A 485 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL A 499 " --> pdb=" O   ALA A 495 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ILE A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 560
      removed outlier: 3.605A  pdb=" N   THR A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 579
    Processing helix  chain 'A' and resid 626 through 631
    Processing helix  chain 'A' and resid 653 through 670
      removed outlier: 3.626A  pdb=" N   VAL A 670 " --> pdb=" O   GLU A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 690
    Processing helix  chain 'A' and resid 691 through 694
      removed outlier: 3.737A  pdb=" N   GLU A 694 " --> pdb=" O   ARG A 691 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 691 through 694'
    Processing helix  chain 'A' and resid 695 through 702
      removed outlier: 3.942A  pdb=" N   GLU A 700 " --> pdb=" O   ALA A 697 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU A 702 " --> pdb=" O   TRP A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 723
      removed outlier: 3.591A  pdb=" N   GLU A 723 " --> pdb=" O   LEU A 719 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 31
    Processing helix  chain 'B' and resid 41 through 48
      removed outlier: 4.243A  pdb=" N   GLN B  48 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 53 through 65
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 75 through 105
      removed outlier: 5.182A  pdb=" N   LEU B  81 " --> pdb=" O   LYS B  77 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   GLY B  82 " --> pdb=" O   GLU B  78 " (cutoff:3.500A)
      Proline residue:  B  96  - end of helix
    Processing helix  chain 'B' and resid 108 through 115
      removed outlier: 3.987A  pdb=" N   GLY B 112 " --> pdb=" O   PRO B 108 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU B 113 " --> pdb=" O   PRO B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 127
      removed outlier: 3.715A  pdb=" N   PHE B 125 " --> pdb=" O   ILE B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 152
    Processing helix  chain 'B' and resid 168 through 196
    Processing helix  chain 'B' and resid 197 through 205
      removed outlier: 4.086A  pdb=" N   PHE B 200 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE B 203 " --> pdb=" O   PHE B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 225
    Processing helix  chain 'B' and resid 225 through 231
    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 308
      removed outlier: 3.543A  pdb=" N   PHE B 295 " --> pdb=" O   PRO B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 313
      removed outlier: 3.744A  pdb=" N   TYR B 313 " --> pdb=" O   LEU B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 366
      removed outlier: 6.430A  pdb=" N   VAL B 341 " --> pdb=" O   HIS B 337 " (cutoff:3.500A)
      removed outlier: 5.834A  pdb=" N   ASP B 342 " --> pdb=" O   LEU B 338 " (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 428
      removed outlier: 3.513A  pdb=" N   CYS B 415 " --> pdb=" O   GLN B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 435
      removed outlier: 4.189A  pdb=" N   SER B 434 " --> pdb=" O   LEU B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 448
      removed outlier: 3.847A  pdb=" N   LEU B 440 " --> pdb=" O   PRO 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: 3.875A  pdb=" N   PHE B 460 " --> pdb=" O   SER B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 481
    Processing helix  chain 'B' and resid 483 through 505
      removed outlier: 3.713A  pdb=" N   LEU B 488 " --> pdb=" O   LEU B 484 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   ILE B 489 " --> pdb=" O   ASP B 485 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   VAL B 499 " --> pdb=" O   ALA B 495 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ILE B 500 " --> pdb=" O   LEU B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 548 through 560
      removed outlier: 3.605A  pdb=" N   THR B 560 " --> pdb=" O   LEU B 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 563 through 579
    Processing helix  chain 'B' and resid 626 through 631
    Processing helix  chain 'B' and resid 653 through 670
      removed outlier: 3.627A  pdb=" N   VAL B 670 " --> pdb=" O   GLU B 666 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 680 through 690
    Processing helix  chain 'B' and resid 691 through 694
      removed outlier: 3.737A  pdb=" N   GLU B 694 " --> pdb=" O   ARG B 691 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 691 through 694'
    Processing helix  chain 'B' and resid 695 through 702
      removed outlier: 3.943A  pdb=" N   GLU B 700 " --> pdb=" O   ALA B 697 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU B 702 " --> pdb=" O   TRP B 699 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 723
      removed outlier: 3.590A  pdb=" N   GLU B 723 " --> pdb=" O   LEU B 719 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20
      removed outlier: 3.817A  pdb=" N   VAL A  18 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   VAL B  18 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 135
      removed outlier: 3.607A  pdb=" N   GLY A 135 " --> pdb=" O   SER A 394 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   SER A 394 " --> pdb=" O   GLY A 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522
      removed outlier: 3.520A  pdb=" N   LYS A 509 " --> pdb=" O   GLN A 539 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU A 511 " --> pdb=" O   ILE A 537 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   ILE A 537 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
      removed outlier: 8.401A  pdb=" N   LYS A 513 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
      removed outlier: 11.976A  pdb=" N   ILE A 535 " --> pdb=" O   LYS A 513 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   LYS A 536 " --> pdb=" O   ILE A 643 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   ASP A 645 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   PHE A 538 " --> pdb=" O   ASP A 645 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 135
      removed outlier: 3.606A  pdb=" N   GLY B 135 " --> pdb=" O   SER B 394 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   SER B 394 " --> pdb=" O   GLY B 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522
      removed outlier: 3.520A  pdb=" N   LYS B 509 " --> pdb=" O   GLN B 539 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU B 511 " --> pdb=" O   ILE B 537 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   ILE B 537 " --> pdb=" O   LEU B 511 " (cutoff:3.500A)
      removed outlier: 8.400A  pdb=" N   LYS B 513 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 11.976A  pdb=" N   ILE B 535 " --> pdb=" O   LYS B 513 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   LYS B 536 " --> pdb=" O   ILE B 643 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   ASP B 645 " --> pdb=" O   LYS B 536 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   PHE B 538 " --> pdb=" O   ASP B 645 " (cutoff:3.500A)

    656 hydrogen bonds defined for protein.
    1902 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: 3.33

  Time building geometry restraints manager: 3.44 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3236
        1.34 -     1.46: 2311
        1.46 -     1.58: 5063
        1.58 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 10688
  Sorted by residual:
  bond pdb=" CA  ILE A 532 "
       pdb=" CB  ILE A 532 "
    ideal  model  delta    sigma   weight residual
    1.537  1.529  0.008 1.29e-02 6.01e+03 4.04e-01
  bond pdb=" C   LEU B  71 "
       pdb=" N   PRO B  72 "
    ideal  model  delta    sigma   weight residual
    1.335  1.342 -0.007 1.28e-02 6.10e+03 3.41e-01
  bond pdb=" C   GLY A 408 "
       pdb=" O   GLY A 408 "
    ideal  model  delta    sigma   weight residual
    1.235  1.243 -0.008 1.35e-02 5.49e+03 3.41e-01
  bond pdb=" C   GLY B 408 "
       pdb=" O   GLY B 408 "
    ideal  model  delta    sigma   weight residual
    1.235  1.243 -0.008 1.35e-02 5.49e+03 3.36e-01
  bond pdb=" N   PRO B 327 "
       pdb=" CA  PRO B 327 "
    ideal  model  delta    sigma   weight residual
    1.459  1.467 -0.008 1.40e-02 5.10e+03 3.20e-01
  ... (remaining 10683 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 14199
        1.03 -     2.07: 245
        2.07 -     3.10: 70
        3.10 -     4.14: 6
        4.14 -     5.17: 12
  Bond angle restraints: 14532
  Sorted by residual:
  angle pdb=" N   THR A 517 "
        pdb=" CA  THR A 517 "
        pdb=" C   THR A 517 "
      ideal   model   delta    sigma   weight residual
     108.34  110.93   -2.59 1.31e+00 5.83e-01 3.90e+00
  angle pdb=" N   THR B 517 "
        pdb=" CA  THR B 517 "
        pdb=" C   THR B 517 "
      ideal   model   delta    sigma   weight residual
     108.34  110.90   -2.56 1.31e+00 5.83e-01 3.81e+00
  angle pdb=" N   SER A  24 "
        pdb=" CA  SER A  24 "
        pdb=" C   SER A  24 "
      ideal   model   delta    sigma   weight residual
     110.53  108.23    2.30 1.29e+00 6.01e-01 3.18e+00
  angle pdb=" N   SER B  24 "
        pdb=" CA  SER B  24 "
        pdb=" C   SER B  24 "
      ideal   model   delta    sigma   weight residual
     110.53  108.26    2.27 1.29e+00 6.01e-01 3.09e+00
  angle pdb=" NE  ARG A  31 "
        pdb=" CZ  ARG A  31 "
        pdb=" NH1 ARG A  31 "
      ideal   model   delta    sigma   weight residual
     121.50  120.00    1.50 1.00e+00 1.00e+00 2.26e+00
  ... (remaining 14527 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.64: 6013
       12.64 -    25.27: 243
       25.27 -    37.91: 68
       37.91 -    50.55: 8
       50.55 -    63.18: 6
  Dihedral angle restraints: 6338
    sinusoidal: 2414
      harmonic: 3924
  Sorted by residual:
  dihedral pdb=" CA  LEU B 184 "
           pdb=" CB  LEU B 184 "
           pdb=" CG  LEU B 184 "
           pdb=" CD1 LEU B 184 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  118.45  -58.45     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" CA  LEU A 184 "
           pdb=" CB  LEU A 184 "
           pdb=" CG  LEU A 184 "
           pdb=" CD1 LEU A 184 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  118.44  -58.44     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" CA  LEU B 422 "
           pdb=" CB  LEU B 422 "
           pdb=" CG  LEU B 422 "
           pdb=" CD1 LEU B 422 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  123.35   56.65     3      1.50e+01 4.44e-03 9.41e+00
  ... (remaining 6335 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 996
       0.025 -    0.050: 406
       0.050 -    0.075: 210
       0.075 -    0.100: 73
       0.100 -    0.126: 43
  Chirality restraints: 1728
  Sorted by residual:
  chirality pdb=" CA  ILE A 532 "
            pdb=" N   ILE A 532 "
            pdb=" C   ILE A 532 "
            pdb=" CB  ILE A 532 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.94e-01
  chirality pdb=" CA  ILE B 532 "
            pdb=" N   ILE B 532 "
            pdb=" C   ILE B 532 "
            pdb=" CB  ILE B 532 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  chirality pdb=" CA  ILE B 290 "
            pdb=" N   ILE B 290 "
            pdb=" C   ILE B 290 "
            pdb=" CB  ILE B 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  ... (remaining 1725 not shown)

  Planarity restraints: 1808
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 542 "   -0.019 5.00e-02 4.00e+02   2.85e-02 1.30e+00
        pdb=" N   PRO A 543 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 543 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 543 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 542 "    0.019 5.00e-02 4.00e+02   2.84e-02 1.29e+00
        pdb=" N   PRO B 543 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO B 543 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 543 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  53 "   -0.018 5.00e-02 4.00e+02   2.69e-02 1.15e+00
        pdb=" N   PRO B  54 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO B  54 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B  54 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1805 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2359
        2.79 -     3.31: 10623
        3.31 -     3.84: 17205
        3.84 -     4.37: 18938
        4.37 -     4.90: 33623
  Nonbonded interactions: 82748
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 495 "
            pdb=" OG1 THR B 498 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   ALA A 495 "
            pdb=" OG1 THR A 498 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OD2 ASP A  83 "
            pdb=" OG1 THR A 410 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" O   LEU B 556 "
            pdb=" OG1 THR B 560 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" O   LEU A 556 "
            pdb=" OG1 THR A 560 "
     model   vdw
     2.317 3.040
  ... (remaining 82743 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.310
  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:          0.560
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     31.440
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
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      :  0.001   0.014  10688  Z= 0.082
  Angle     :  0.399   5.170  14532  Z= 0.224
  Chirality :  0.039   0.126   1728
  Planarity :  0.003   0.029   1808
  Dihedral  :  7.882  63.182   3826
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  4.94 %
    Favored  : 94.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.25), residues: 1352
  helix:  2.34 (0.19), residues: 908
  sheet:  3.14 (0.70), residues: 52
  loop : -0.75 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B  70 
 HIS   0.002   0.000   HIS B  25 
 PHE   0.005   0.001   PHE B 269 
 TYR   0.008   0.001   TYR A 340 
 ARG   0.001   0.000   ARG B  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14039 (  656)
  hydrogen bonds       : angle       4.64272 ( 1902)
  covalent geometry    : bond        0.00141 (10688)
  covalent geometry    : angle       0.39944 (14532)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 302
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 MET cc_start: 0.7309 (tpt) cc_final: 0.7014 (tpp)
REVERT: A  633 MET cc_start: 0.7954 (tpt) cc_final: 0.7561 (tpp)
REVERT: A  669 ASP cc_start: 0.7836 (t0) cc_final: 0.7532 (t0)
REVERT: B  357 MET cc_start: 0.7373 (tpt) cc_final: 0.7051 (tpp)
REVERT: B  482 LEU cc_start: 0.9013 (mt) cc_final: 0.8790 (tt)
REVERT: B  633 MET cc_start: 0.8036 (tpt) cc_final: 0.7537 (tpp)
REVERT: B  669 ASP cc_start: 0.7739 (t0) cc_final: 0.7502 (t0)
REVERT: B  719 LEU cc_start: 0.9397 (mt) cc_final: 0.9189 (mm)
  outliers start: 12
  outliers final: 0
  residues processed: 306
  average time/residue: 0.2429
  time to fit residues: 101.5390
Evaluate side-chains
  144 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    7.9990
   chunk 103 optimal weight:   40.0000
   chunk 57 optimal weight:    0.0970
   chunk 35 optimal weight:   30.0000
   chunk 69 optimal weight:   10.0000
   chunk 55 optimal weight:    0.6980
   chunk 106 optimal weight:   50.0000
   chunk 41 optimal weight:    0.0030
   chunk 64 optimal weight:   20.0000
   chunk 79 optimal weight:   20.0000
   chunk 123 optimal weight:    0.4980
   overall best weight:    1.8590

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

Flipped N/Q/H residues before XYZ refinement:
A 722 GLN
B 447 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.084816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.062417 restraints weight = 49582.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.064673 restraints weight = 25561.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.066150 restraints weight = 16499.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10688  Z= 0.109
  Angle     :  0.524   7.822  14532  Z= 0.261
  Chirality :  0.042   0.148   1728
  Planarity :  0.004   0.031   1808
  Dihedral  :  2.932  12.593   1456
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.24), residues: 1352
  helix:  2.19 (0.18), residues: 906
  sheet:  3.37 (0.72), residues: 52
  loop : -0.52 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  70 
 HIS   0.002   0.001   HIS A  25 
 PHE   0.010   0.001   PHE A 452 
 TYR   0.016   0.001   TYR A 123 
 ARG   0.003   0.000   ARG A 571 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03551 (  656)
  hydrogen bonds       : angle       3.85478 ( 1902)
  covalent geometry    : bond        0.00226 (10688)
  covalent geometry    : angle       0.52389 (14532)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 1.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8923 (pt) cc_final: 0.8487 (pt)
REVERT: A  180 MET cc_start: 0.8793 (tpp) cc_final: 0.8356 (mmm)
REVERT: A  357 MET cc_start: 0.8988 (tpt) cc_final: 0.8487 (tpp)
REVERT: A  448 LEU cc_start: 0.9408 (tp) cc_final: 0.9139 (tp)
REVERT: A  451 MET cc_start: 0.8522 (mmp) cc_final: 0.8053 (tpp)
REVERT: A  633 MET cc_start: 0.8414 (tpt) cc_final: 0.8056 (tpp)
REVERT: B  121 ILE cc_start: 0.9564 (mm) cc_final: 0.9300 (pt)
REVERT: B  132 ILE cc_start: 0.9065 (pt) cc_final: 0.8711 (pt)
REVERT: B  180 MET cc_start: 0.8714 (tpp) cc_final: 0.8414 (mmm)
REVERT: B  299 MET cc_start: 0.9110 (mmp) cc_final: 0.8115 (tmm)
REVERT: B  357 MET cc_start: 0.8968 (tpt) cc_final: 0.8461 (tpp)
REVERT: B  448 LEU cc_start: 0.9394 (tp) cc_final: 0.9134 (tp)
REVERT: B  451 MET cc_start: 0.8662 (mmp) cc_final: 0.8225 (tpp)
REVERT: B  482 LEU cc_start: 0.8954 (mt) cc_final: 0.8579 (tt)
REVERT: B  633 MET cc_start: 0.8608 (tpt) cc_final: 0.8130 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.2013
  time to fit residues: 52.8494
Evaluate side-chains
  136 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 9 optimal weight:   20.0000
   chunk 105 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9980
   chunk 82 optimal weight:    8.9990
   chunk 16 optimal weight:   20.0000
   chunk 35 optimal weight:    9.9990
   chunk 98 optimal weight:   10.0000
   chunk 37 optimal weight:   40.0000
   chunk 124 optimal weight:   30.0000
   chunk 90 optimal weight:   20.0000
   chunk 119 optimal weight:    8.9990
   overall best weight:    6.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.081644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.058774 restraints weight = 51252.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.060794 restraints weight = 26606.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.062057 restraints weight = 17453.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10688  Z= 0.156
  Angle     :  0.543   6.514  14532  Z= 0.276
  Chirality :  0.043   0.140   1728
  Planarity :  0.004   0.032   1808
  Dihedral  :  3.232  14.280   1456
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.38 %
    Favored  : 97.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.13 (0.24), residues: 1352
  helix:  2.15 (0.18), residues: 906
  sheet:  2.79 (0.74), residues: 52
  loop : -0.57 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 699 
 HIS   0.005   0.001   HIS B  25 
 PHE   0.011   0.001   PHE B  76 
 TYR   0.018   0.001   TYR B  79 
 ARG   0.004   0.000   ARG B 691 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03422 (  656)
  hydrogen bonds       : angle       3.78162 ( 1902)
  covalent geometry    : bond        0.00341 (10688)
  covalent geometry    : angle       0.54286 (14532)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 172
  time to evaluate  : 1.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8992 (pt) cc_final: 0.8566 (pt)
REVERT: A  177 LYS cc_start: 0.9694 (mmpt) cc_final: 0.9379 (mttt)
REVERT: A  180 MET cc_start: 0.8822 (tpp) cc_final: 0.8363 (mmm)
REVERT: A  299 MET cc_start: 0.9099 (mmp) cc_final: 0.8068 (tmm)
REVERT: A  357 MET cc_start: 0.9081 (tpt) cc_final: 0.8503 (tpp)
REVERT: A  435 LEU cc_start: 0.9302 (mm) cc_final: 0.9015 (mm)
REVERT: A  448 LEU cc_start: 0.9505 (tp) cc_final: 0.9268 (tp)
REVERT: A  451 MET cc_start: 0.8752 (mmp) cc_final: 0.8366 (tpp)
REVERT: A  633 MET cc_start: 0.8679 (tpt) cc_final: 0.8232 (tpp)
REVERT: A  665 LYS cc_start: 0.9061 (tptp) cc_final: 0.8741 (tppt)
REVERT: A  669 ASP cc_start: 0.7951 (m-30) cc_final: 0.7601 (m-30)
REVERT: B  121 ILE cc_start: 0.9584 (mm) cc_final: 0.9334 (pt)
REVERT: B  132 ILE cc_start: 0.9126 (pt) cc_final: 0.8806 (pt)
REVERT: B  180 MET cc_start: 0.8810 (tpp) cc_final: 0.8244 (mmm)
REVERT: B  299 MET cc_start: 0.9149 (mmp) cc_final: 0.8172 (tmm)
REVERT: B  357 MET cc_start: 0.9048 (tpt) cc_final: 0.8438 (tpp)
REVERT: B  435 LEU cc_start: 0.9290 (mm) cc_final: 0.8997 (mm)
REVERT: B  448 LEU cc_start: 0.9470 (tp) cc_final: 0.9253 (tp)
REVERT: B  451 MET cc_start: 0.8757 (mmp) cc_final: 0.8475 (tpp)
REVERT: B  482 LEU cc_start: 0.9003 (mt) cc_final: 0.8636 (tt)
REVERT: B  633 MET cc_start: 0.8815 (tpt) cc_final: 0.8268 (tpp)
REVERT: B  665 LYS cc_start: 0.9160 (tptp) cc_final: 0.8847 (tppt)
  outliers start: 2
  outliers final: 2
  residues processed: 174
  average time/residue: 0.2254
  time to fit residues: 57.0786
Evaluate side-chains
  131 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 129
  time to evaluate  : 1.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 103 optimal weight:    9.9990
   chunk 84 optimal weight:   30.0000
   chunk 39 optimal weight:   50.0000
   chunk 128 optimal weight:    8.9990
   chunk 102 optimal weight:    6.9990
   chunk 25 optimal weight:   40.0000
   chunk 38 optimal weight:   30.0000
   chunk 108 optimal weight:   40.0000
   chunk 35 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  33 HIS
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  33 HIS
B 504 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.080368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.057411 restraints weight = 50818.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.059361 restraints weight = 26978.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.060604 restraints weight = 17977.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10688  Z= 0.169
  Angle     :  0.557   6.836  14532  Z= 0.282
  Chirality :  0.043   0.136   1728
  Planarity :  0.004   0.037   1808
  Dihedral  :  3.406  15.531   1456
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.24), residues: 1352
  helix:  2.01 (0.18), residues: 910
  sheet:  2.53 (0.74), residues: 52
  loop : -0.49 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 699 
 HIS   0.007   0.001   HIS B  25 
 PHE   0.020   0.001   PHE B 452 
 TYR   0.018   0.002   TYR A  79 
 ARG   0.003   0.000   ARG B 691 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03371 (  656)
  hydrogen bonds       : angle       3.82032 ( 1902)
  covalent geometry    : bond        0.00372 (10688)
  covalent geometry    : angle       0.55732 (14532)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.9041 (pt) cc_final: 0.8666 (pt)
REVERT: A  177 LYS cc_start: 0.9704 (mmpt) cc_final: 0.9383 (mttt)
REVERT: A  180 MET cc_start: 0.8878 (tpp) cc_final: 0.8438 (mmm)
REVERT: A  253 ASN cc_start: 0.9042 (m-40) cc_final: 0.8793 (p0)
REVERT: A  299 MET cc_start: 0.9110 (mmp) cc_final: 0.8104 (tmm)
REVERT: A  357 MET cc_start: 0.9049 (tpt) cc_final: 0.8643 (tpp)
REVERT: A  435 LEU cc_start: 0.9341 (mm) cc_final: 0.9090 (mm)
REVERT: A  451 MET cc_start: 0.8775 (mmp) cc_final: 0.8333 (tpp)
REVERT: A  452 PHE cc_start: 0.8720 (m-10) cc_final: 0.8216 (t80)
REVERT: A  633 MET cc_start: 0.8675 (tpt) cc_final: 0.8214 (tpp)
REVERT: A  665 LYS cc_start: 0.9083 (tptp) cc_final: 0.8729 (tppt)
REVERT: A  669 ASP cc_start: 0.7957 (m-30) cc_final: 0.7560 (m-30)
REVERT: B  132 ILE cc_start: 0.9171 (pt) cc_final: 0.8893 (pt)
REVERT: B  180 MET cc_start: 0.8900 (tpp) cc_final: 0.8538 (mmm)
REVERT: B  253 ASN cc_start: 0.9006 (m-40) cc_final: 0.8781 (p0)
REVERT: B  299 MET cc_start: 0.9169 (mmp) cc_final: 0.8227 (tmm)
REVERT: B  357 MET cc_start: 0.9066 (tpt) cc_final: 0.8695 (tpp)
REVERT: B  435 LEU cc_start: 0.9317 (mm) cc_final: 0.9070 (mm)
REVERT: B  448 LEU cc_start: 0.9489 (tp) cc_final: 0.9279 (tp)
REVERT: B  451 MET cc_start: 0.8799 (mmp) cc_final: 0.8342 (tpp)
REVERT: B  482 LEU cc_start: 0.9083 (mt) cc_final: 0.8689 (tt)
REVERT: B  497 LEU cc_start: 0.9122 (mt) cc_final: 0.8877 (tt)
REVERT: B  633 MET cc_start: 0.8824 (tpt) cc_final: 0.8266 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1869
  time to fit residues: 45.7422
Evaluate side-chains
  123 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 103 optimal weight:   20.0000
   chunk 111 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 18 optimal weight:   40.0000
   chunk 128 optimal weight:    9.9990
   chunk 94 optimal weight:   30.0000
   chunk 116 optimal weight:    5.9990
   chunk 80 optimal weight:   40.0000
   chunk 79 optimal weight:    7.9990
   chunk 52 optimal weight:    9.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 648 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.078503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.055943 restraints weight = 51380.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.057831 restraints weight = 27078.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.059080 restraints weight = 17894.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.3966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10688  Z= 0.143
  Angle     :  0.543   6.269  14532  Z= 0.275
  Chirality :  0.043   0.144   1728
  Planarity :  0.004   0.039   1808
  Dihedral  :  3.484  19.029   1456
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.04 (0.24), residues: 1352
  helix:  2.02 (0.18), residues: 906
  sheet:  3.08 (0.90), residues: 38
  loop : -0.33 (0.33), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  70 
 HIS   0.006   0.001   HIS A  25 
 PHE   0.024   0.001   PHE B 351 
 TYR   0.017   0.001   TYR A 552 
 ARG   0.003   0.000   ARG B 691 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03303 (  656)
  hydrogen bonds       : angle       3.76086 ( 1902)
  covalent geometry    : bond        0.00314 (10688)
  covalent geometry    : angle       0.54258 (14532)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8998 (pt) cc_final: 0.8570 (pt)
REVERT: A  151 LEU cc_start: 0.9326 (mm) cc_final: 0.9114 (mm)
REVERT: A  177 LYS cc_start: 0.9720 (mmpt) cc_final: 0.9388 (mttt)
REVERT: A  180 MET cc_start: 0.8830 (tpp) cc_final: 0.8427 (mmm)
REVERT: A  228 TYR cc_start: 0.8117 (m-80) cc_final: 0.7272 (m-80)
REVERT: A  253 ASN cc_start: 0.9107 (m-40) cc_final: 0.8820 (p0)
REVERT: A  299 MET cc_start: 0.9126 (mmp) cc_final: 0.8133 (tmm)
REVERT: A  357 MET cc_start: 0.9093 (tpt) cc_final: 0.8521 (tpp)
REVERT: A  435 LEU cc_start: 0.9278 (mm) cc_final: 0.8963 (mm)
REVERT: A  440 LEU cc_start: 0.9582 (mm) cc_final: 0.9025 (tp)
REVERT: A  448 LEU cc_start: 0.9513 (tp) cc_final: 0.8555 (tp)
REVERT: A  451 MET cc_start: 0.8745 (mmp) cc_final: 0.8332 (tpp)
REVERT: A  452 PHE cc_start: 0.8885 (m-10) cc_final: 0.7929 (m-80)
REVERT: A  509 LYS cc_start: 0.8560 (mttt) cc_final: 0.8138 (mmmt)
REVERT: A  633 MET cc_start: 0.8699 (tpt) cc_final: 0.8257 (tpp)
REVERT: A  665 LYS cc_start: 0.9126 (tptp) cc_final: 0.8743 (tppt)
REVERT: A  669 ASP cc_start: 0.7974 (m-30) cc_final: 0.7525 (m-30)
REVERT: B  132 ILE cc_start: 0.9143 (pt) cc_final: 0.8825 (pt)
REVERT: B  180 MET cc_start: 0.8837 (tpp) cc_final: 0.8510 (mmm)
REVERT: B  207 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8502 (tm-30)
REVERT: B  253 ASN cc_start: 0.9059 (m-40) cc_final: 0.8779 (p0)
REVERT: B  299 MET cc_start: 0.9167 (mmp) cc_final: 0.8244 (tmm)
REVERT: B  357 MET cc_start: 0.9102 (tpt) cc_final: 0.8563 (tpp)
REVERT: B  435 LEU cc_start: 0.9299 (mm) cc_final: 0.9012 (mm)
REVERT: B  448 LEU cc_start: 0.9523 (tp) cc_final: 0.9320 (tp)
REVERT: B  451 MET cc_start: 0.8833 (mmp) cc_final: 0.8486 (tpp)
REVERT: B  633 MET cc_start: 0.8842 (tpt) cc_final: 0.8336 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.2007
  time to fit residues: 49.0211
Evaluate side-chains
  131 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 72 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 103 optimal weight:   30.0000
   chunk 21 optimal weight:   30.0000
   chunk 101 optimal weight:   10.0000
   chunk 25 optimal weight:   40.0000
   chunk 135 optimal weight:    0.1980
   chunk 85 optimal weight:    5.9990
   chunk 126 optimal weight:   20.0000
   chunk 19 optimal weight:    8.9990
   overall best weight:    7.0390

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 648 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.077525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.055239 restraints weight = 52795.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.057111 restraints weight = 27764.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.058353 restraints weight = 18327.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.4345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10688  Z= 0.160
  Angle     :  0.569   6.373  14532  Z= 0.285
  Chirality :  0.044   0.170   1728
  Planarity :  0.004   0.045   1808
  Dihedral  :  3.572  18.289   1456
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.15 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.24), residues: 1352
  helix:  2.06 (0.18), residues: 906
  sheet:  2.89 (0.90), residues: 38
  loop : -0.40 (0.34), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 699 
 HIS   0.005   0.001   HIS A  25 
 PHE   0.011   0.001   PHE A 269 
 TYR   0.021   0.002   TYR B 552 
 ARG   0.003   0.000   ARG A 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03392 (  656)
  hydrogen bonds       : angle       3.77695 ( 1902)
  covalent geometry    : bond        0.00354 (10688)
  covalent geometry    : angle       0.56894 (14532)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 1.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.9008 (pt) cc_final: 0.8629 (pt)
REVERT: A  228 TYR cc_start: 0.8105 (m-80) cc_final: 0.7687 (m-80)
REVERT: A  253 ASN cc_start: 0.9071 (m-40) cc_final: 0.8813 (p0)
REVERT: A  299 MET cc_start: 0.9144 (mmp) cc_final: 0.8181 (tmm)
REVERT: A  357 MET cc_start: 0.9049 (tpt) cc_final: 0.8648 (tpp)
REVERT: A  435 LEU cc_start: 0.9281 (mm) cc_final: 0.9056 (mm)
REVERT: A  448 LEU cc_start: 0.9552 (tp) cc_final: 0.9312 (tp)
REVERT: A  451 MET cc_start: 0.8813 (mmp) cc_final: 0.8371 (tpp)
REVERT: A  484 LEU cc_start: 0.8654 (mt) cc_final: 0.7937 (tt)
REVERT: A  509 LYS cc_start: 0.8637 (mttt) cc_final: 0.8231 (mmmt)
REVERT: A  633 MET cc_start: 0.8660 (tpt) cc_final: 0.8247 (tpp)
REVERT: A  665 LYS cc_start: 0.9129 (tptp) cc_final: 0.8907 (tppt)
REVERT: B  132 ILE cc_start: 0.9148 (pt) cc_final: 0.8848 (pt)
REVERT: B  151 LEU cc_start: 0.9385 (mm) cc_final: 0.9162 (mt)
REVERT: B  180 MET cc_start: 0.8863 (tpp) cc_final: 0.8536 (mmm)
REVERT: B  253 ASN cc_start: 0.9048 (m-40) cc_final: 0.8791 (p0)
REVERT: B  299 MET cc_start: 0.9188 (mmp) cc_final: 0.8296 (tmm)
REVERT: B  357 MET cc_start: 0.9102 (tpt) cc_final: 0.8677 (tpp)
REVERT: B  451 MET cc_start: 0.8830 (mmp) cc_final: 0.8384 (tpp)
REVERT: B  452 PHE cc_start: 0.8776 (m-10) cc_final: 0.8203 (t80)
REVERT: B  488 LEU cc_start: 0.8874 (tt) cc_final: 0.8660 (tp)
REVERT: B  509 LYS cc_start: 0.8566 (mttt) cc_final: 0.8295 (mmmt)
REVERT: B  633 MET cc_start: 0.8818 (tpt) cc_final: 0.8301 (tpp)
REVERT: B  665 LYS cc_start: 0.9072 (tppt) cc_final: 0.8699 (tppt)
  outliers start: 1
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2647
  time to fit residues: 64.4715
Evaluate side-chains
  127 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 107 optimal weight:   50.0000
   chunk 127 optimal weight:   30.0000
   chunk 85 optimal weight:   50.0000
   chunk 105 optimal weight:   30.0000
   chunk 34 optimal weight:   20.0000
   chunk 57 optimal weight:    0.0980
   chunk 117 optimal weight:    6.9990
   chunk 114 optimal weight:    8.9990
   chunk 91 optimal weight:   40.0000
   chunk 61 optimal weight:    8.9990
   chunk 106 optimal weight:   40.0000
   overall best weight:    9.0190

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.075910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.053520 restraints weight = 53256.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.055369 restraints weight = 27532.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.056559 restraints weight = 18152.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.4841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10688  Z= 0.196
  Angle     :  0.607   7.541  14532  Z= 0.306
  Chirality :  0.045   0.152   1728
  Planarity :  0.004   0.040   1808
  Dihedral  :  3.852  19.461   1456
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.24), residues: 1352
  helix:  1.87 (0.18), residues: 908
  sheet:  2.59 (0.89), residues: 38
  loop : -0.34 (0.35), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  70 
 HIS   0.009   0.002   HIS A  25 
 PHE   0.017   0.002   PHE A 213 
 TYR   0.023   0.002   TYR B 552 
 ARG   0.004   0.001   ARG A 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03636 (  656)
  hydrogen bonds       : angle       3.90665 ( 1902)
  covalent geometry    : bond        0.00428 (10688)
  covalent geometry    : angle       0.60713 (14532)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.9004 (pt) cc_final: 0.8633 (pt)
REVERT: A  213 PHE cc_start: 0.8850 (t80) cc_final: 0.8459 (t80)
REVERT: A  253 ASN cc_start: 0.9107 (m-40) cc_final: 0.8834 (p0)
REVERT: A  299 MET cc_start: 0.9176 (mmp) cc_final: 0.8216 (tmm)
REVERT: A  357 MET cc_start: 0.9082 (tpt) cc_final: 0.8535 (tpp)
REVERT: A  435 LEU cc_start: 0.9291 (mm) cc_final: 0.9006 (mm)
REVERT: A  440 LEU cc_start: 0.9543 (mm) cc_final: 0.9045 (tp)
REVERT: A  452 PHE cc_start: 0.8815 (m-10) cc_final: 0.8271 (t80)
REVERT: A  484 LEU cc_start: 0.8685 (mt) cc_final: 0.7962 (tt)
REVERT: A  633 MET cc_start: 0.8661 (tpt) cc_final: 0.8277 (tpp)
REVERT: B  132 ILE cc_start: 0.9127 (pt) cc_final: 0.8821 (pt)
REVERT: B  151 LEU cc_start: 0.9411 (mm) cc_final: 0.9175 (mt)
REVERT: B  180 MET cc_start: 0.8861 (tpp) cc_final: 0.8516 (mmm)
REVERT: B  253 ASN cc_start: 0.9076 (m-40) cc_final: 0.8812 (p0)
REVERT: B  299 MET cc_start: 0.9200 (mmp) cc_final: 0.8317 (tmm)
REVERT: B  357 MET cc_start: 0.9146 (tpt) cc_final: 0.8617 (tpp)
REVERT: B  448 LEU cc_start: 0.9567 (tp) cc_final: 0.9366 (tp)
REVERT: B  488 LEU cc_start: 0.8925 (tt) cc_final: 0.8601 (tp)
REVERT: B  633 MET cc_start: 0.8771 (tpt) cc_final: 0.8302 (tpp)
REVERT: B  665 LYS cc_start: 0.9129 (tppt) cc_final: 0.8743 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2399
  time to fit residues: 55.1696
Evaluate side-chains
  115 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 109 optimal weight:   30.0000
   chunk 31 optimal weight:   40.0000
   chunk 126 optimal weight:    0.0050
   chunk 22 optimal weight:   10.0000
   chunk 42 optimal weight:    7.9990
   chunk 13 optimal weight:   40.0000
   chunk 112 optimal weight:   10.0000
   chunk 72 optimal weight:   20.0000
   chunk 44 optimal weight:    0.4980
   chunk 85 optimal weight:    8.9990
   chunk 102 optimal weight:   20.0000
   overall best weight:    5.5002

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.076769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.054384 restraints weight = 52531.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.056269 restraints weight = 27336.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.057491 restraints weight = 17999.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.4973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10688  Z= 0.140
  Angle     :  0.575   6.854  14532  Z= 0.287
  Chirality :  0.044   0.179   1728
  Planarity :  0.004   0.040   1808
  Dihedral  :  3.775  19.996   1456
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.24), residues: 1352
  helix:  1.90 (0.18), residues: 904
  sheet:  2.60 (0.89), residues: 38
  loop : -0.33 (0.34), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 699 
 HIS   0.012   0.001   HIS B  25 
 PHE   0.025   0.001   PHE A 452 
 TYR   0.022   0.001   TYR B 552 
 ARG   0.004   0.000   ARG A 691 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03470 (  656)
  hydrogen bonds       : angle       3.78759 ( 1902)
  covalent geometry    : bond        0.00304 (10688)
  covalent geometry    : angle       0.57519 (14532)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8942 (pt) cc_final: 0.8542 (pt)
REVERT: A  213 PHE cc_start: 0.8831 (t80) cc_final: 0.8428 (t80)
REVERT: A  253 ASN cc_start: 0.9096 (m-40) cc_final: 0.8851 (p0)
REVERT: A  299 MET cc_start: 0.9203 (mmp) cc_final: 0.8261 (tmm)
REVERT: A  357 MET cc_start: 0.9038 (tpt) cc_final: 0.8641 (tpp)
REVERT: A  435 LEU cc_start: 0.9323 (mm) cc_final: 0.9046 (mm)
REVERT: A  440 LEU cc_start: 0.9522 (mm) cc_final: 0.8956 (tp)
REVERT: A  448 LEU cc_start: 0.9555 (tt) cc_final: 0.9180 (tt)
REVERT: A  452 PHE cc_start: 0.9028 (m-10) cc_final: 0.8337 (t80)
REVERT: A  484 LEU cc_start: 0.8661 (mt) cc_final: 0.8061 (tt)
REVERT: A  509 LYS cc_start: 0.8533 (mttt) cc_final: 0.8306 (mmmt)
REVERT: A  633 MET cc_start: 0.8617 (tpt) cc_final: 0.8268 (tpp)
REVERT: A  669 ASP cc_start: 0.7979 (m-30) cc_final: 0.7773 (m-30)
REVERT: B  132 ILE cc_start: 0.9050 (pt) cc_final: 0.8737 (pt)
REVERT: B  180 MET cc_start: 0.8836 (tpp) cc_final: 0.8527 (mmm)
REVERT: B  253 ASN cc_start: 0.9074 (m-40) cc_final: 0.8797 (p0)
REVERT: B  299 MET cc_start: 0.9211 (mmp) cc_final: 0.8333 (tmm)
REVERT: B  351 PHE cc_start: 0.9243 (t80) cc_final: 0.8982 (t80)
REVERT: B  357 MET cc_start: 0.9082 (tpt) cc_final: 0.8764 (tpp)
REVERT: B  376 ILE cc_start: 0.9213 (mt) cc_final: 0.8968 (mm)
REVERT: B  451 MET cc_start: 0.7975 (tpp) cc_final: 0.7694 (tpp)
REVERT: B  488 LEU cc_start: 0.8913 (tt) cc_final: 0.8587 (tp)
REVERT: B  633 MET cc_start: 0.8757 (tpt) cc_final: 0.8309 (tpp)
REVERT: B  665 LYS cc_start: 0.9146 (tppt) cc_final: 0.8756 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.1944
  time to fit residues: 45.0108
Evaluate side-chains
  118 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 1.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 131 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   chunk 66 optimal weight:    6.9990
   chunk 102 optimal weight:    9.9990
   chunk 43 optimal weight:   20.0000
   chunk 44 optimal weight:    5.9990
   chunk 78 optimal weight:    6.9990
   chunk 82 optimal weight:    5.9990
   chunk 133 optimal weight:    5.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.077532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.054945 restraints weight = 52240.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.056865 restraints weight = 27319.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.058106 restraints weight = 18059.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.5013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10688  Z= 0.112
  Angle     :  0.559   7.638  14532  Z= 0.276
  Chirality :  0.044   0.171   1728
  Planarity :  0.004   0.039   1808
  Dihedral  :  3.653  19.549   1456
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.24), residues: 1352
  helix:  1.89 (0.18), residues: 906
  sheet:  2.81 (0.89), residues: 38
  loop : -0.30 (0.34), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 699 
 HIS   0.009   0.001   HIS B  25 
 PHE   0.016   0.001   PHE A 452 
 TYR   0.021   0.001   TYR B 552 
 ARG   0.006   0.000   ARG A 691 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03263 (  656)
  hydrogen bonds       : angle       3.72175 ( 1902)
  covalent geometry    : bond        0.00240 (10688)
  covalent geometry    : angle       0.55911 (14532)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8869 (pt) cc_final: 0.8416 (pt)
REVERT: A  213 PHE cc_start: 0.8833 (t80) cc_final: 0.8337 (t80)
REVERT: A  253 ASN cc_start: 0.9079 (m-40) cc_final: 0.8817 (p0)
REVERT: A  299 MET cc_start: 0.9188 (mmp) cc_final: 0.8276 (tmm)
REVERT: A  357 MET cc_start: 0.9036 (tpt) cc_final: 0.8442 (tpp)
REVERT: A  435 LEU cc_start: 0.9295 (mm) cc_final: 0.9013 (mm)
REVERT: A  440 LEU cc_start: 0.9507 (mm) cc_final: 0.8904 (tp)
REVERT: A  448 LEU cc_start: 0.9539 (tt) cc_final: 0.9151 (tt)
REVERT: A  451 MET cc_start: 0.8310 (tpp) cc_final: 0.8026 (tpp)
REVERT: A  452 PHE cc_start: 0.9037 (m-10) cc_final: 0.8335 (t80)
REVERT: A  484 LEU cc_start: 0.8697 (mt) cc_final: 0.7968 (tt)
REVERT: A  633 MET cc_start: 0.8535 (tpt) cc_final: 0.8185 (tpp)
REVERT: A  669 ASP cc_start: 0.7862 (m-30) cc_final: 0.7605 (m-30)
REVERT: B  132 ILE cc_start: 0.8992 (pt) cc_final: 0.8612 (pt)
REVERT: B  253 ASN cc_start: 0.9069 (m-40) cc_final: 0.8805 (p0)
REVERT: B  276 LYS cc_start: 0.8375 (tttt) cc_final: 0.7948 (ptmt)
REVERT: B  299 MET cc_start: 0.9209 (mmp) cc_final: 0.8337 (tmm)
REVERT: B  351 PHE cc_start: 0.9233 (t80) cc_final: 0.8952 (t80)
REVERT: B  357 MET cc_start: 0.9088 (tpt) cc_final: 0.8500 (tpp)
REVERT: B  440 LEU cc_start: 0.9454 (mm) cc_final: 0.8891 (tp)
REVERT: B  488 LEU cc_start: 0.8910 (tt) cc_final: 0.8521 (tp)
REVERT: B  633 MET cc_start: 0.8702 (tpt) cc_final: 0.8262 (tpp)
REVERT: B  665 LYS cc_start: 0.9127 (tppt) cc_final: 0.8719 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.2081
  time to fit residues: 49.4064
Evaluate side-chains
  129 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 47 optimal weight:   20.0000
   chunk 120 optimal weight:    9.9990
   chunk 123 optimal weight:    0.6980
   chunk 52 optimal weight:    7.9990
   chunk 85 optimal weight:   30.0000
   chunk 79 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 134 optimal weight:    0.8980
   overall best weight:    3.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.077734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.055013 restraints weight = 52157.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.056927 restraints weight = 27365.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.058155 restraints weight = 18118.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.5112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10688  Z= 0.112
  Angle     :  0.571   7.953  14532  Z= 0.279
  Chirality :  0.044   0.186   1728
  Planarity :  0.004   0.040   1808
  Dihedral  :  3.657  19.210   1456
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.24), residues: 1352
  helix:  1.86 (0.18), residues: 902
  sheet:  3.27 (0.89), residues: 36
  loop : -0.38 (0.34), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 699 
 HIS   0.008   0.001   HIS B  25 
 PHE   0.023   0.001   PHE A 351 
 TYR   0.019   0.001   TYR B 552 
 ARG   0.004   0.000   ARG A 691 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03235 (  656)
  hydrogen bonds       : angle       3.77168 ( 1902)
  covalent geometry    : bond        0.00244 (10688)
  covalent geometry    : angle       0.57072 (14532)

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8848 (pt) cc_final: 0.8436 (pt)
REVERT: A  213 PHE cc_start: 0.8771 (t80) cc_final: 0.8472 (t80)
REVERT: A  253 ASN cc_start: 0.9077 (m-40) cc_final: 0.8839 (p0)
REVERT: A  299 MET cc_start: 0.9193 (mmp) cc_final: 0.8284 (tmm)
REVERT: A  357 MET cc_start: 0.9003 (tpt) cc_final: 0.8583 (tpp)
REVERT: A  381 CYS cc_start: 0.9245 (m) cc_final: 0.8699 (m)
REVERT: A  484 LEU cc_start: 0.8659 (mt) cc_final: 0.8012 (tt)
REVERT: A  633 MET cc_start: 0.8520 (tpt) cc_final: 0.8171 (tpp)
REVERT: B  132 ILE cc_start: 0.8969 (pt) cc_final: 0.8609 (pt)
REVERT: B  253 ASN cc_start: 0.9064 (m-40) cc_final: 0.8790 (p0)
REVERT: B  276 LYS cc_start: 0.8390 (tttt) cc_final: 0.7956 (ptmt)
REVERT: B  299 MET cc_start: 0.9215 (mmp) cc_final: 0.8345 (tmm)
REVERT: B  357 MET cc_start: 0.9063 (tpt) cc_final: 0.8669 (tpp)
REVERT: B  435 LEU cc_start: 0.9291 (mm) cc_final: 0.9013 (mm)
REVERT: B  440 LEU cc_start: 0.9453 (mm) cc_final: 0.8880 (tp)
REVERT: B  633 MET cc_start: 0.8723 (tpt) cc_final: 0.8277 (tpp)
REVERT: B  665 LYS cc_start: 0.9132 (tppt) cc_final: 0.8783 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1832
  time to fit residues: 43.6322
Evaluate side-chains
  121 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 1.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 120 optimal weight:    8.9990
   chunk 130 optimal weight:   10.0000
   chunk 99 optimal weight:    8.9990
   chunk 100 optimal weight:    6.9990
   chunk 27 optimal weight:   50.0000
   chunk 78 optimal weight:   20.0000
   chunk 23 optimal weight:   20.0000
   chunk 25 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 36 optimal weight:   20.0000
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.076080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.053440 restraints weight = 52343.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.055220 restraints weight = 28246.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.056333 restraints weight = 19054.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.5392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10688  Z= 0.174
  Angle     :  0.615   7.559  14532  Z= 0.307
  Chirality :  0.045   0.178   1728
  Planarity :  0.004   0.040   1808
  Dihedral  :  3.866  18.988   1456
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.24), residues: 1352
  helix:  1.81 (0.18), residues: 898
  sheet:  3.16 (0.88), residues: 36
  loop : -0.50 (0.34), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  70 
 HIS   0.012   0.001   HIS B  25 
 PHE   0.024   0.001   PHE A 452 
 TYR   0.020   0.002   TYR B 552 
 ARG   0.004   0.001   ARG A 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03548 (  656)
  hydrogen bonds       : angle       3.93757 ( 1902)
  covalent geometry    : bond        0.00383 (10688)
  covalent geometry    : angle       0.61517 (14532)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3740.35 seconds
wall clock time: 67 minutes 20.49 seconds (4040.49 seconds total)