Starting phenix.real_space_refine
on Fri Feb 14 13:25:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lh3_23335/02_2025/7lh3_23335.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lh3_23335/02_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_23335/02_2025/7lh3_23335.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lh3_23335/02_2025/7lh3_23335.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lh3_23335/02_2025/7lh3_23335.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lh3_23335/02_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-5592/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: 9.88, per 1000 atoms: 0.95
  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: 2.68
  Conformation dependent library (CDL) restraints added in 1.2 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: 1.17
  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: 3.44

  Time building geometry restraints manager: 3.08 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: 0.05
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:             0.860
  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:          0.490
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     29.770
  Find NCS groups from input model:        0.190
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.370
-------------------------------------------------------------------------------
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= 0.090
  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 

*********************** 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  : 1.232 
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: 0.2458
  time to fit residues: 102.5749
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  : 1.253 
-------------------------------------------------------------------------------
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 = 42)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.062414 restraints weight = 49582.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.064665 restraints weight = 25526.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.066067 restraints weight = 16519.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
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= 0.143
  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 

*********************** 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  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8927 (pt) cc_final: 0.8488 (pt)
REVERT: A  180 MET cc_start: 0.8793 (tpp) cc_final: 0.8358 (mmm)
REVERT: A  357 MET cc_start: 0.8993 (tpt) cc_final: 0.8493 (tpp)
REVERT: A  448 LEU cc_start: 0.9402 (tp) cc_final: 0.9133 (tp)
REVERT: A  451 MET cc_start: 0.8521 (mmp) cc_final: 0.8052 (tpp)
REVERT: A  633 MET cc_start: 0.8443 (tpt) cc_final: 0.8089 (tpp)
REVERT: B  121 ILE cc_start: 0.9563 (mm) cc_final: 0.9302 (pt)
REVERT: B  132 ILE cc_start: 0.9066 (pt) cc_final: 0.8705 (pt)
REVERT: B  180 MET cc_start: 0.8714 (tpp) cc_final: 0.8415 (mmm)
REVERT: B  299 MET cc_start: 0.9114 (mmp) cc_final: 0.8121 (tmm)
REVERT: B  357 MET cc_start: 0.8974 (tpt) cc_final: 0.8470 (tpp)
REVERT: B  448 LEU cc_start: 0.9389 (tp) cc_final: 0.9128 (tp)
REVERT: B  451 MET cc_start: 0.8663 (mmp) cc_final: 0.8228 (tpp)
REVERT: B  482 LEU cc_start: 0.8955 (mt) cc_final: 0.8580 (tt)
REVERT: B  633 MET cc_start: 0.8633 (tpt) cc_final: 0.8162 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.2077
  time to fit residues: 54.3577
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  : 1.168 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 105 optimal weight:    0.9990
   chunk 109 optimal weight:    7.9990
   chunk 82 optimal weight:    0.0670
   chunk 16 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 98 optimal weight:   30.0000
   chunk 37 optimal weight:    8.9990
   chunk 124 optimal weight:   30.0000
   chunk 90 optimal weight:   40.0000
   chunk 119 optimal weight:    8.9990
   overall best weight:    5.0126

-------------------------------------------------------------------------------
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 = 0.3677 r_free = 0.3677 target = 0.082677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.059898 restraints weight = 50728.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.061977 restraints weight = 26378.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.063341 restraints weight = 17241.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.3049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10688  Z= 0.184
  Angle     :  0.514   6.579  14532  Z= 0.262
  Chirality :  0.042   0.141   1728
  Planarity :  0.004   0.031   1808
  Dihedral  :  3.148  13.654   1456
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.29 %
    Favored  : 97.53 %
  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:  2.17 (0.25), residues: 1352
  helix:  2.18 (0.18), residues: 906
  sheet:  2.86 (0.74), residues: 52
  loop : -0.56 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  70 
 HIS   0.004   0.001   HIS A  25 
 PHE   0.009   0.001   PHE B  76 
 TYR   0.014   0.001   TYR A 228 
 ARG   0.004   0.000   ARG A 236 

*********************** 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
  171 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 169
  time to evaluate  : 1.143 
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: 0.8967 (pt) cc_final: 0.8529 (pt)
REVERT: A  177 LYS cc_start: 0.9692 (mmpt) cc_final: 0.9379 (mttt)
REVERT: A  180 MET cc_start: 0.8804 (tpp) cc_final: 0.8353 (mmm)
REVERT: A  299 MET cc_start: 0.9087 (mmp) cc_final: 0.8044 (tmm)
REVERT: A  357 MET cc_start: 0.9045 (tpt) cc_final: 0.8449 (tpp)
REVERT: A  435 LEU cc_start: 0.9280 (mm) cc_final: 0.8993 (mm)
REVERT: A  448 LEU cc_start: 0.9496 (tp) cc_final: 0.9261 (tp)
REVERT: A  451 MET cc_start: 0.8707 (mmp) cc_final: 0.8282 (tpp)
REVERT: A  633 MET cc_start: 0.8614 (tpt) cc_final: 0.8180 (tpp)
REVERT: A  665 LYS cc_start: 0.9045 (tptp) cc_final: 0.8708 (tppt)
REVERT: A  669 ASP cc_start: 0.7940 (m-30) cc_final: 0.7586 (m-30)
REVERT: B  121 ILE cc_start: 0.9579 (mm) cc_final: 0.9329 (pt)
REVERT: B  132 ILE cc_start: 0.9100 (pt) cc_final: 0.8759 (pt)
REVERT: B  180 MET cc_start: 0.8791 (tpp) cc_final: 0.8221 (mmm)
REVERT: B  299 MET cc_start: 0.9145 (mmp) cc_final: 0.8172 (tmm)
REVERT: B  357 MET cc_start: 0.9005 (tpt) cc_final: 0.8411 (tpp)
REVERT: B  435 LEU cc_start: 0.9263 (mm) cc_final: 0.8974 (mm)
REVERT: B  448 LEU cc_start: 0.9458 (tp) cc_final: 0.9244 (tp)
REVERT: B  451 MET cc_start: 0.8694 (mmp) cc_final: 0.8410 (tpp)
REVERT: B  482 LEU cc_start: 0.8991 (mt) cc_final: 0.8635 (tt)
REVERT: B  633 MET cc_start: 0.8744 (tpt) cc_final: 0.8215 (tpp)
REVERT: B  665 LYS cc_start: 0.9161 (tptp) cc_final: 0.8841 (tppt)
  outliers start: 2
  outliers final: 2
  residues processed: 171
  average time/residue: 0.2041
  time to fit residues: 51.1751
Evaluate side-chains
  128 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
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:   40.0000
   chunk 103 optimal weight:   30.0000
   chunk 84 optimal weight:   40.0000
   chunk 39 optimal weight:    2.9990
   chunk 128 optimal weight:   10.0000
   chunk 102 optimal weight:    7.9990
   chunk 25 optimal weight:   20.0000
   chunk 38 optimal weight:   10.0000
   chunk 108 optimal weight:   30.0000
   chunk 35 optimal weight:    8.9990
   chunk 23 optimal weight:   20.0000
   overall best weight:    7.9994

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.078958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.056346 restraints weight = 51031.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.058257 restraints weight = 26946.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.059480 restraints weight = 17823.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.3744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10688  Z= 0.256
  Angle     :  0.577   6.421  14532  Z= 0.291
  Chirality :  0.043   0.130   1728
  Planarity :  0.004   0.037   1808
  Dihedral  :  3.454  15.697   1456
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  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:  1.94 (0.24), residues: 1352
  helix:  1.97 (0.18), residues: 910
  sheet:  2.47 (0.73), residues: 52
  loop : -0.51 (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   0.015   0.002   PHE B 452 
 TYR   0.023   0.002   TYR A 552 
 ARG   0.003   0.000   ARG A 236 

*********************** 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  : 1.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.9046 (pt) cc_final: 0.8665 (pt)
REVERT: A  177 LYS cc_start: 0.9717 (mmpt) cc_final: 0.9388 (mttt)
REVERT: A  180 MET cc_start: 0.8847 (tpp) cc_final: 0.8416 (mmm)
REVERT: A  228 TYR cc_start: 0.7757 (m-80) cc_final: 0.7221 (m-80)
REVERT: A  253 ASN cc_start: 0.9064 (m-40) cc_final: 0.8791 (p0)
REVERT: A  299 MET cc_start: 0.9118 (mmp) cc_final: 0.8126 (tmm)
REVERT: A  357 MET cc_start: 0.9089 (tpt) cc_final: 0.8687 (tpp)
REVERT: A  435 LEU cc_start: 0.9359 (mm) cc_final: 0.9110 (mm)
REVERT: A  451 MET cc_start: 0.8853 (mmp) cc_final: 0.8398 (tpp)
REVERT: A  452 PHE cc_start: 0.8762 (m-10) cc_final: 0.8271 (t80)
REVERT: A  633 MET cc_start: 0.8736 (tpt) cc_final: 0.8300 (tpp)
REVERT: A  665 LYS cc_start: 0.9094 (tptp) cc_final: 0.8740 (tppt)
REVERT: A  669 ASP cc_start: 0.7979 (m-30) cc_final: 0.7553 (m-30)
REVERT: B  132 ILE cc_start: 0.9188 (pt) cc_final: 0.8892 (pt)
REVERT: B  180 MET cc_start: 0.8872 (tpp) cc_final: 0.8517 (mmm)
REVERT: B  204 TYR cc_start: 0.8407 (m-80) cc_final: 0.8179 (m-80)
REVERT: B  253 ASN cc_start: 0.9038 (m-40) cc_final: 0.8782 (p0)
REVERT: B  299 MET cc_start: 0.9174 (mmp) cc_final: 0.8225 (tmm)
REVERT: B  357 MET cc_start: 0.9066 (tpt) cc_final: 0.8701 (tpp)
REVERT: B  435 LEU cc_start: 0.9337 (mm) cc_final: 0.9102 (mm)
REVERT: B  451 MET cc_start: 0.8892 (mmp) cc_final: 0.8332 (tpp)
REVERT: B  482 LEU cc_start: 0.9040 (mt) cc_final: 0.8643 (tt)
REVERT: B  497 LEU cc_start: 0.9141 (mt) cc_final: 0.8886 (tt)
REVERT: B  633 MET cc_start: 0.8873 (tpt) cc_final: 0.8354 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1963
  time to fit residues: 47.7871
Evaluate side-chains
  125 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 68 optimal weight:    0.7980
   chunk 70 optimal weight:   30.0000
   chunk 18 optimal weight:   30.0000
   chunk 128 optimal weight:    9.9990
   chunk 94 optimal weight:    9.9990
   chunk 116 optimal weight:    9.9990
   chunk 80 optimal weight:   30.0000
   chunk 79 optimal weight:   20.0000
   chunk 52 optimal weight:    0.0870
   overall best weight:    6.1764

-------------------------------------------------------------------------------
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 = 0.3608 r_free = 0.3608 target = 0.079493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.056654 restraints weight = 51538.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.058598 restraints weight = 27014.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.059868 restraints weight = 17862.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.3972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10688  Z= 0.208
  Angle     :  0.549   7.031  14532  Z= 0.274
  Chirality :  0.043   0.147   1728
  Planarity :  0.004   0.038   1808
  Dihedral  :  3.505  19.201   1456
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.24), residues: 1352
  helix:  1.95 (0.18), residues: 908
  sheet:  3.02 (0.90), residues: 38
  loop : -0.33 (0.33), residues: 406

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   0.019   0.001   PHE A 452 
 TYR   0.015   0.001   TYR A 552 
 ARG   0.003   0.000   ARG B 691 

*********************** 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
  169 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.9002 (pt) cc_final: 0.8578 (pt)
REVERT: A  177 LYS cc_start: 0.9710 (mmpt) cc_final: 0.9386 (mttt)
REVERT: A  180 MET cc_start: 0.8840 (tpp) cc_final: 0.8436 (mmm)
REVERT: A  253 ASN cc_start: 0.9087 (m-40) cc_final: 0.8817 (p0)
REVERT: A  299 MET cc_start: 0.9129 (mmp) cc_final: 0.8155 (tmm)
REVERT: A  357 MET cc_start: 0.9076 (tpt) cc_final: 0.8505 (tpp)
REVERT: A  435 LEU cc_start: 0.9325 (mm) cc_final: 0.9027 (mm)
REVERT: A  448 LEU cc_start: 0.9511 (tt) cc_final: 0.9086 (tt)
REVERT: A  451 MET cc_start: 0.8716 (mmp) cc_final: 0.8469 (tpp)
REVERT: A  452 PHE cc_start: 0.9035 (m-10) cc_final: 0.8259 (t80)
REVERT: A  633 MET cc_start: 0.8659 (tpt) cc_final: 0.8205 (tpp)
REVERT: A  665 LYS cc_start: 0.9114 (tptp) cc_final: 0.8729 (tppt)
REVERT: A  669 ASP cc_start: 0.7977 (m-30) cc_final: 0.7547 (m-30)
REVERT: B  121 ILE cc_start: 0.9527 (mm) cc_final: 0.9279 (pt)
REVERT: B  132 ILE cc_start: 0.9143 (pt) cc_final: 0.8817 (pt)
REVERT: B  180 MET cc_start: 0.8836 (tpp) cc_final: 0.8487 (mmm)
REVERT: B  204 TYR cc_start: 0.8518 (m-80) cc_final: 0.8218 (m-80)
REVERT: B  253 ASN cc_start: 0.9057 (m-40) cc_final: 0.8787 (p0)
REVERT: B  299 MET cc_start: 0.9166 (mmp) cc_final: 0.8252 (tmm)
REVERT: B  357 MET cc_start: 0.9128 (tpt) cc_final: 0.8578 (tpp)
REVERT: B  435 LEU cc_start: 0.9286 (mm) cc_final: 0.8990 (mm)
REVERT: B  448 LEU cc_start: 0.9490 (tp) cc_final: 0.9254 (tp)
REVERT: B  451 MET cc_start: 0.8788 (mmp) cc_final: 0.8470 (tpp)
REVERT: B  633 MET cc_start: 0.8819 (tpt) cc_final: 0.8296 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.2045
  time to fit residues: 51.0409
Evaluate side-chains
  126 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.326 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 72 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 103 optimal weight:   40.0000
   chunk 21 optimal weight:    6.9990
   chunk 101 optimal weight:    8.9990
   chunk 25 optimal weight:    8.9990
   chunk 135 optimal weight:    0.9980
   chunk 85 optimal weight:    8.9990
   chunk 126 optimal weight:   20.0000
   chunk 19 optimal weight:    9.9990
   overall best weight:    6.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 648 GLN
B 648 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.077710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.055171 restraints weight = 52501.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.057047 restraints weight = 27844.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.058281 restraints weight = 18564.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.4352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10688  Z= 0.228
  Angle     :  0.574   6.698  14532  Z= 0.286
  Chirality :  0.044   0.175   1728
  Planarity :  0.004   0.036   1808
  Dihedral  :  3.577  18.238   1456
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.32 %
    Favored  : 98.59 %
  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:  1.93 (0.24), residues: 1352
  helix:  1.96 (0.18), residues: 906
  sheet:  2.86 (0.90), residues: 38
  loop : -0.42 (0.34), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 699 
 HIS   0.005   0.001   HIS A  25 
 PHE   0.019   0.001   PHE A 452 
 TYR   0.023   0.002   TYR A 552 
 ARG   0.002   0.000   ARG B 691 

*********************** 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
  165 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 164
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.9009 (pt) cc_final: 0.8612 (pt)
REVERT: A  151 LEU cc_start: 0.9350 (mm) cc_final: 0.9142 (mm)
REVERT: A  253 ASN cc_start: 0.9106 (m-40) cc_final: 0.8822 (p0)
REVERT: A  299 MET cc_start: 0.9150 (mmp) cc_final: 0.8189 (tmm)
REVERT: A  357 MET cc_start: 0.9065 (tpt) cc_final: 0.8665 (tpp)
REVERT: A  435 LEU cc_start: 0.9326 (mm) cc_final: 0.9122 (mm)
REVERT: A  448 LEU cc_start: 0.9507 (tt) cc_final: 0.9189 (tt)
REVERT: A  451 MET cc_start: 0.8703 (mmp) cc_final: 0.8359 (tpp)
REVERT: A  452 PHE cc_start: 0.8923 (m-10) cc_final: 0.8265 (t80)
REVERT: A  484 LEU cc_start: 0.8649 (mt) cc_final: 0.7959 (tt)
REVERT: A  633 MET cc_start: 0.8710 (tpt) cc_final: 0.8283 (tpp)
REVERT: B  103 MET cc_start: 0.9139 (ppp) cc_final: 0.8845 (ppp)
REVERT: B  132 ILE cc_start: 0.9121 (pt) cc_final: 0.8794 (pt)
REVERT: B  180 MET cc_start: 0.8812 (tpp) cc_final: 0.8485 (mmm)
REVERT: B  253 ASN cc_start: 0.9084 (m-40) cc_final: 0.8793 (p0)
REVERT: B  299 MET cc_start: 0.9194 (mmp) cc_final: 0.8297 (tmm)
REVERT: B  357 MET cc_start: 0.9075 (tpt) cc_final: 0.8694 (tpp)
REVERT: B  451 MET cc_start: 0.8786 (mmp) cc_final: 0.8385 (tpp)
REVERT: B  452 PHE cc_start: 0.8790 (m-10) cc_final: 0.8191 (t80)
REVERT: B  633 MET cc_start: 0.8826 (tpt) cc_final: 0.8343 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 165
  average time/residue: 0.1986
  time to fit residues: 48.6351
Evaluate side-chains
  125 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.394 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 127 optimal weight:    0.0070
   chunk 85 optimal weight:   50.0000
   chunk 105 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 57 optimal weight:    0.0470
   chunk 117 optimal weight:    8.9990
   chunk 114 optimal weight:    2.9990
   chunk 91 optimal weight:   20.0000
   chunk 61 optimal weight:    2.9990
   chunk 106 optimal weight:    6.9990
   overall best weight:    2.4102

-------------------------------------------------------------------------------
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 = 0.3589 r_free = 0.3589 target = 0.078807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.056312 restraints weight = 52195.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.058287 restraints weight = 27186.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.059570 restraints weight = 17851.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.4391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10688  Z= 0.138
  Angle     :  0.525   7.337  14532  Z= 0.258
  Chirality :  0.043   0.169   1728
  Planarity :  0.004   0.041   1808
  Dihedral  :  3.452  18.096   1456
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    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:  2.11 (0.24), residues: 1352
  helix:  2.07 (0.18), residues: 906
  sheet:  2.96 (0.88), residues: 38
  loop : -0.26 (0.34), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 472 
 HIS   0.004   0.001   HIS A  25 
 PHE   0.019   0.001   PHE B 351 
 TYR   0.008   0.001   TYR A 123 
 ARG   0.005   0.000   ARG A 150 

*********************** 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
  165 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8921 (pt) cc_final: 0.8419 (pt)
REVERT: A  253 ASN cc_start: 0.9108 (m-40) cc_final: 0.8819 (p0)
REVERT: A  299 MET cc_start: 0.9160 (mmp) cc_final: 0.8208 (tmm)
REVERT: A  357 MET cc_start: 0.9047 (tpt) cc_final: 0.8440 (tpp)
REVERT: A  435 LEU cc_start: 0.9285 (mm) cc_final: 0.9029 (mm)
REVERT: A  440 LEU cc_start: 0.9526 (mm) cc_final: 0.8953 (tp)
REVERT: A  448 LEU cc_start: 0.9493 (tt) cc_final: 0.9187 (tt)
REVERT: A  452 PHE cc_start: 0.8909 (m-10) cc_final: 0.8231 (t80)
REVERT: A  484 LEU cc_start: 0.8633 (mt) cc_final: 0.7887 (tt)
REVERT: A  509 LYS cc_start: 0.8484 (mttt) cc_final: 0.8176 (mmmt)
REVERT: A  633 MET cc_start: 0.8628 (tpt) cc_final: 0.8260 (tpp)
REVERT: A  669 ASP cc_start: 0.7942 (m-30) cc_final: 0.7732 (m-30)
REVERT: A  691 ARG cc_start: 0.8645 (mmp80) cc_final: 0.8423 (mmp80)
REVERT: B  132 ILE cc_start: 0.9037 (pt) cc_final: 0.8600 (pt)
REVERT: B  180 MET cc_start: 0.8764 (tpp) cc_final: 0.8422 (mmm)
REVERT: B  253 ASN cc_start: 0.9067 (m-40) cc_final: 0.8783 (p0)
REVERT: B  299 MET cc_start: 0.9198 (mmp) cc_final: 0.8308 (tmm)
REVERT: B  357 MET cc_start: 0.9102 (tpt) cc_final: 0.8505 (tpp)
REVERT: B  445 ILE cc_start: 0.9267 (mm) cc_final: 0.9055 (mm)
REVERT: B  451 MET cc_start: 0.8687 (mmp) cc_final: 0.8396 (tpp)
REVERT: B  452 PHE cc_start: 0.8776 (m-10) cc_final: 0.7980 (m-80)
REVERT: B  633 MET cc_start: 0.8782 (tpt) cc_final: 0.8316 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.1948
  time to fit residues: 48.0417
Evaluate side-chains
  130 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 126 optimal weight:   20.0000
   chunk 22 optimal weight:   40.0000
   chunk 42 optimal weight:    6.9990
   chunk 13 optimal weight:   30.0000
   chunk 112 optimal weight:    5.9990
   chunk 72 optimal weight:    0.0670
   chunk 44 optimal weight:    0.2980
   chunk 85 optimal weight:   50.0000
   chunk 102 optimal weight:    6.9990
   overall best weight:    2.8122

-------------------------------------------------------------------------------
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 = 0.3586 r_free = 0.3586 target = 0.078859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.056328 restraints weight = 51757.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.058302 restraints weight = 27053.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.059571 restraints weight = 17824.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.4505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10688  Z= 0.142
  Angle     :  0.545   7.904  14532  Z= 0.265
  Chirality :  0.043   0.169   1728
  Planarity :  0.004   0.038   1808
  Dihedral  :  3.439  17.642   1456
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  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:  2.06 (0.24), residues: 1352
  helix:  2.02 (0.18), residues: 908
  sheet:  2.97 (0.88), residues: 38
  loop : -0.27 (0.34), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  70 
 HIS   0.005   0.001   HIS A  25 
 PHE   0.027   0.001   PHE B 351 
 TYR   0.016   0.001   TYR B 552 
 ARG   0.004   0.000   ARG A 150 

*********************** 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
  168 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8896 (pt) cc_final: 0.8440 (pt)
REVERT: A  253 ASN cc_start: 0.9084 (m-40) cc_final: 0.8815 (p0)
REVERT: A  299 MET cc_start: 0.9157 (mmp) cc_final: 0.8206 (tmm)
REVERT: A  357 MET cc_start: 0.8974 (tpt) cc_final: 0.8546 (tpp)
REVERT: A  435 LEU cc_start: 0.9296 (mm) cc_final: 0.9033 (mm)
REVERT: A  448 LEU cc_start: 0.9556 (tt) cc_final: 0.9348 (tt)
REVERT: A  451 MET cc_start: 0.7940 (tpp) cc_final: 0.7590 (tpp)
REVERT: A  452 PHE cc_start: 0.8814 (m-10) cc_final: 0.8167 (t80)
REVERT: A  484 LEU cc_start: 0.8632 (mt) cc_final: 0.7982 (tt)
REVERT: A  509 LYS cc_start: 0.8567 (mttt) cc_final: 0.8251 (mmmt)
REVERT: A  633 MET cc_start: 0.8585 (tpt) cc_final: 0.8208 (tpp)
REVERT: A  669 ASP cc_start: 0.7895 (m-30) cc_final: 0.7643 (m-30)
REVERT: A  691 ARG cc_start: 0.8628 (mmp80) cc_final: 0.8402 (mmp80)
REVERT: B  132 ILE cc_start: 0.9021 (pt) cc_final: 0.8644 (pt)
REVERT: B  180 MET cc_start: 0.8789 (tpp) cc_final: 0.8425 (mmm)
REVERT: B  253 ASN cc_start: 0.9048 (m-40) cc_final: 0.8777 (p0)
REVERT: B  299 MET cc_start: 0.9189 (mmp) cc_final: 0.8298 (tmm)
REVERT: B  355 ILE cc_start: 0.9482 (tt) cc_final: 0.9260 (mm)
REVERT: B  357 MET cc_start: 0.8995 (tpt) cc_final: 0.8552 (tpp)
REVERT: B  452 PHE cc_start: 0.8764 (m-10) cc_final: 0.8213 (t80)
REVERT: B  633 MET cc_start: 0.8759 (tpt) cc_final: 0.8278 (tpp)
REVERT: B  665 LYS cc_start: 0.9106 (tppt) cc_final: 0.8720 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.2022
  time to fit residues: 50.2447
Evaluate side-chains
  132 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 57 optimal weight:    0.4980
   chunk 48 optimal weight:    8.9990
   chunk 49 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 102 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   chunk 78 optimal weight:   40.0000
   chunk 82 optimal weight:   10.0000
   chunk 133 optimal weight:    8.9990
   overall best weight:    6.4988

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.077288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.054640 restraints weight = 52701.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.056528 restraints weight = 27904.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.057745 restraints weight = 18495.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.4770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10688  Z= 0.217
  Angle     :  0.583   8.174  14532  Z= 0.288
  Chirality :  0.044   0.155   1728
  Planarity :  0.004   0.037   1808
  Dihedral  :  3.609  17.961   1456
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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:  1.93 (0.24), residues: 1352
  helix:  1.95 (0.18), residues: 904
  sheet:  2.79 (0.88), residues: 38
  loop : -0.38 (0.34), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  70 
 HIS   0.007   0.001   HIS A  25 
 PHE   0.016   0.001   PHE A 452 
 TYR   0.026   0.001   TYR B 552 
 ARG   0.004   0.000   ARG A 150 

*********************** 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
  159 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 1.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8940 (pt) cc_final: 0.8514 (pt)
REVERT: A  253 ASN cc_start: 0.9096 (m-40) cc_final: 0.8816 (p0)
REVERT: A  299 MET cc_start: 0.9182 (mmp) cc_final: 0.8232 (tmm)
REVERT: A  357 MET cc_start: 0.9089 (tpt) cc_final: 0.8498 (tpp)
REVERT: A  435 LEU cc_start: 0.9311 (mm) cc_final: 0.9039 (mm)
REVERT: A  448 LEU cc_start: 0.9597 (tt) cc_final: 0.9349 (tt)
REVERT: A  452 PHE cc_start: 0.8937 (m-10) cc_final: 0.8237 (t80)
REVERT: A  484 LEU cc_start: 0.8670 (mt) cc_final: 0.7956 (tt)
REVERT: A  633 MET cc_start: 0.8670 (tpt) cc_final: 0.8280 (tpp)
REVERT: A  691 ARG cc_start: 0.8642 (mmp80) cc_final: 0.8414 (mmp80)
REVERT: B  132 ILE cc_start: 0.9057 (pt) cc_final: 0.8690 (pt)
REVERT: B  180 MET cc_start: 0.8804 (tpp) cc_final: 0.8449 (mmm)
REVERT: B  253 ASN cc_start: 0.9066 (m-40) cc_final: 0.8799 (p0)
REVERT: B  276 LYS cc_start: 0.8384 (tttt) cc_final: 0.7953 (ptmt)
REVERT: B  299 MET cc_start: 0.9196 (mmp) cc_final: 0.8324 (tmm)
REVERT: B  355 ILE cc_start: 0.9487 (tt) cc_final: 0.9276 (mm)
REVERT: B  357 MET cc_start: 0.9175 (tpt) cc_final: 0.8634 (tpp)
REVERT: B  381 CYS cc_start: 0.9284 (m) cc_final: 0.8913 (m)
REVERT: B  445 ILE cc_start: 0.9276 (mm) cc_final: 0.9046 (mm)
REVERT: B  452 PHE cc_start: 0.8873 (m-10) cc_final: 0.8053 (m-80)
REVERT: B  633 MET cc_start: 0.8800 (tpt) cc_final: 0.8294 (tpp)
REVERT: B  665 LYS cc_start: 0.9126 (tppt) cc_final: 0.8747 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.2009
  time to fit residues: 47.4894
Evaluate side-chains
  126 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.283 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 47 optimal weight:    0.0770
   chunk 120 optimal weight:    6.9990
   chunk 123 optimal weight:    0.0870
   chunk 52 optimal weight:    0.8980
   chunk 85 optimal weight:    8.9990
   chunk 79 optimal weight:   10.0000
   chunk 49 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   chunk 72 optimal weight:    7.9990
   chunk 134 optimal weight:    5.9990
   overall best weight:    2.8120

-------------------------------------------------------------------------------
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 = 0.3581 r_free = 0.3581 target = 0.078339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.055634 restraints weight = 51686.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.057563 restraints weight = 27352.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.058817 restraints weight = 18137.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.4858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10688  Z= 0.145
  Angle     :  0.561   7.259  14532  Z= 0.273
  Chirality :  0.043   0.171   1728
  Planarity :  0.004   0.038   1808
  Dihedral  :  3.549  19.545   1456
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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:  1.95 (0.25), residues: 1352
  helix:  1.93 (0.18), residues: 902
  sheet:  2.87 (0.87), residues: 38
  loop : -0.26 (0.34), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 699 
 HIS   0.010   0.001   HIS B  25 
 PHE   0.023   0.001   PHE A 452 
 TYR   0.014   0.001   TYR B 552 
 ARG   0.004   0.000   ARG B 691 

********************** 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
  159 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8880 (pt) cc_final: 0.8452 (pt)
REVERT: A  253 ASN cc_start: 0.9079 (m-40) cc_final: 0.8784 (p0)
REVERT: A  299 MET cc_start: 0.9173 (mmp) cc_final: 0.8236 (tmm)
REVERT: A  357 MET cc_start: 0.8984 (tpt) cc_final: 0.8553 (tpp)
REVERT: A  435 LEU cc_start: 0.9297 (mm) cc_final: 0.9011 (mm)
REVERT: A  484 LEU cc_start: 0.8591 (mt) cc_final: 0.7972 (tt)
REVERT: A  509 LYS cc_start: 0.8515 (mttt) cc_final: 0.8268 (mmmt)
REVERT: A  633 MET cc_start: 0.8591 (tpt) cc_final: 0.8207 (tpp)
REVERT: A  691 ARG cc_start: 0.8618 (mmp80) cc_final: 0.8390 (mmp80)
REVERT: B  132 ILE cc_start: 0.8993 (pt) cc_final: 0.8631 (pt)
REVERT: B  180 MET cc_start: 0.8747 (tpp) cc_final: 0.8360 (mmm)
REVERT: B  253 ASN cc_start: 0.9076 (m-40) cc_final: 0.8805 (p0)
REVERT: B  276 LYS cc_start: 0.8448 (tttt) cc_final: 0.8018 (ptmt)
REVERT: B  299 MET cc_start: 0.9197 (mmp) cc_final: 0.8311 (tmm)
REVERT: B  357 MET cc_start: 0.9074 (tpt) cc_final: 0.8670 (tpp)
REVERT: B  451 MET cc_start: 0.8132 (tpp) cc_final: 0.7919 (tpp)
REVERT: B  452 PHE cc_start: 0.8905 (m-10) cc_final: 0.8202 (m-80)
REVERT: B  633 MET cc_start: 0.8769 (tpt) cc_final: 0.8286 (tpp)
REVERT: B  665 LYS cc_start: 0.9123 (tppt) cc_final: 0.8746 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.1941
  time to fit residues: 45.8211
Evaluate side-chains
  138 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 120 optimal weight:    9.9990
   chunk 130 optimal weight:    6.9990
   chunk 99 optimal weight:    0.4980
   chunk 100 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0010
   chunk 78 optimal weight:   40.0000
   chunk 23 optimal weight:    2.9990
   chunk 25 optimal weight:   50.0000
   chunk 29 optimal weight:   10.0000
   chunk 36 optimal weight:   20.0000
   overall best weight:    3.6992

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.077978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.055206 restraints weight = 51205.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.057123 restraints weight = 27226.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.058329 restraints weight = 18123.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.4958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10688  Z= 0.158
  Angle     :  0.554   7.706  14532  Z= 0.271
  Chirality :  0.043   0.166   1728
  Planarity :  0.004   0.038   1808
  Dihedral  :  3.524  18.743   1456
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.24), residues: 1352
  helix:  1.96 (0.18), residues: 902
  sheet:  2.88 (0.87), residues: 38
  loop : -0.29 (0.34), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 699 
 HIS   0.012   0.001   HIS B  25 
 PHE   0.020   0.001   PHE A 452 
 TYR   0.016   0.001   TYR B 552 
 ARG   0.003   0.000   ARG A 236 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3187.30 seconds
wall clock time: 58 minutes 12.55 seconds (3492.55 seconds total)