Starting phenix.real_space_refine
on Wed Mar  4 02:42:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lh3_23335/03_2026/7lh3_23335.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lh3_23335/03_2026/7lh3_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lh3_23335/03_2026/7lh3_23335.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lh3_23335/03_2026/7lh3_23335.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lh3_23335/03_2026/7lh3_23335.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lh3_23335/03_2026/7lh3_23335.map"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: {'ASN:plan1': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 29
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.02, per 1000 atoms: 0.38
  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: 0.74
  Conformation dependent library (CDL) restraints added in 481.9 milliseconds
  

  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: 0.25
  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: 1.43

  Time building geometry restraints manager: 1.05 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.930
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.014  10688  Z= 0.082
  Angle     :  0.399   5.170  14532  Z= 0.224
  Chirality :  0.039   0.126   1728
  Planarity :  0.003   0.029   1808
  Dihedral  :  7.882  63.182   3826
  Min Nonbonded Distance : 2.258

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

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  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
 ARG   0.001   0.000   ARG B  58 
 TYR   0.008   0.001   TYR A 340 
 PHE   0.005   0.001   PHE B 269 
 TRP   0.003   0.000   TRP B  70 
 HIS   0.002   0.000   HIS B  25 

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

*********************** 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  : 0.308 
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: 0.7740 (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: 0.0975
  time to fit residues: 41.5613
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  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:   40.0000
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:   40.0000
   chunk 55 optimal weight:    4.9990
   overall best weight:    4.5386

-------------------------------------------------------------------------------
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 = 0.3677 r_free = 0.3677 target = 0.082797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.060664 restraints weight = 49652.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.062780 restraints weight = 25669.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.064176 restraints weight = 16656.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.064997 restraints weight = 12483.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.065571 restraints weight = 10434.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.2541

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= 0.131
  Angle     :  0.548   8.234  14532  Z= 0.273
  Chirality :  0.043   0.149   1728
  Planarity :  0.004   0.031   1808
  Dihedral  :  2.998  13.381   1456
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.24), residues: 1352
  helix:  2.24 (0.18), residues: 902
  sheet:  3.15 (0.73), residues: 52
  loop : -0.53 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 571 
 TYR   0.016   0.001   TYR A 123 
 PHE   0.008   0.001   PHE B 198 
 TRP   0.004   0.001   TRP B  70 
 HIS   0.003   0.001   HIS A  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10688)
  covalent geometry    : angle       0.54762 (14532)
  hydrogen bonds       : bond        0.03568 (  656)
  hydrogen bonds       : angle       3.90375 ( 1902)

*********************** 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
  181 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8946 (pt) cc_final: 0.8543 (pt)
REVERT: A  180 MET cc_start: 0.8807 (tpp) cc_final: 0.8330 (mmm)
REVERT: A  184 LEU cc_start: 0.9588 (tt) cc_final: 0.9384 (tp)
REVERT: A  357 MET cc_start: 0.9027 (tpt) cc_final: 0.8540 (tpp)
REVERT: A  448 LEU cc_start: 0.9441 (tp) cc_final: 0.9180 (tp)
REVERT: A  451 MET cc_start: 0.8607 (mmp) cc_final: 0.8187 (tpp)
REVERT: A  633 MET cc_start: 0.8332 (tpt) cc_final: 0.7978 (tpp)
REVERT: B  121 ILE cc_start: 0.9601 (mm) cc_final: 0.9347 (pt)
REVERT: B  132 ILE cc_start: 0.9092 (pt) cc_final: 0.8775 (pt)
REVERT: B  180 MET cc_start: 0.8768 (tpp) cc_final: 0.8457 (mmm)
REVERT: B  299 MET cc_start: 0.9087 (mmp) cc_final: 0.8086 (tmm)
REVERT: B  357 MET cc_start: 0.9003 (tpt) cc_final: 0.8515 (tpp)
REVERT: B  448 LEU cc_start: 0.9432 (tp) cc_final: 0.9180 (tp)
REVERT: B  451 MET cc_start: 0.8663 (mmp) cc_final: 0.8305 (tpp)
REVERT: B  482 LEU cc_start: 0.8990 (mt) cc_final: 0.8617 (tt)
REVERT: B  633 MET cc_start: 0.8508 (tpt) cc_final: 0.8008 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.0885
  time to fit residues: 23.8368
Evaluate side-chains
  134 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 122 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 49 optimal weight:    1.9990
   chunk 111 optimal weight:    8.9990
   chunk 37 optimal weight:   30.0000
   chunk 10 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 42 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 53 optimal weight:    8.9990
   chunk 17 optimal weight:   50.0000
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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 = 0.3653 r_free = 0.3653 target = 0.081455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.058641 restraints weight = 50559.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.060643 restraints weight = 26317.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.061950 restraints weight = 17291.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.062769 restraints weight = 13177.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.063213 restraints weight = 11088.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10688  Z= 0.150
  Angle     :  0.528   6.435  14532  Z= 0.269
  Chirality :  0.042   0.141   1728
  Planarity :  0.004   0.030   1808
  Dihedral  :  3.200  14.357   1456
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.24), residues: 1352
  helix:  2.22 (0.18), residues: 906
  sheet:  2.80 (0.75), residues: 52
  loop : -0.60 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 236 
 TYR   0.011   0.001   TYR A 123 
 PHE   0.014   0.001   PHE B 693 
 TRP   0.008   0.001   TRP A 699 
 HIS   0.005   0.001   HIS A  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (10688)
  covalent geometry    : angle       0.52845 (14532)
  hydrogen bonds       : bond        0.03376 (  656)
  hydrogen bonds       : angle       3.79191 ( 1902)

*********************** 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
  170 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8999 (pt) cc_final: 0.8595 (pt)
REVERT: A  180 MET cc_start: 0.8764 (tpp) cc_final: 0.8342 (mmm)
REVERT: A  299 MET cc_start: 0.9067 (mmp) cc_final: 0.8030 (tmm)
REVERT: A  357 MET cc_start: 0.9073 (tpt) cc_final: 0.8496 (tpp)
REVERT: A  435 LEU cc_start: 0.9301 (mm) cc_final: 0.9015 (mm)
REVERT: A  448 LEU cc_start: 0.9504 (tp) cc_final: 0.9267 (tp)
REVERT: A  451 MET cc_start: 0.8719 (mmp) cc_final: 0.8367 (tpp)
REVERT: A  633 MET cc_start: 0.8562 (tpt) cc_final: 0.8113 (tpp)
REVERT: A  665 LYS cc_start: 0.9045 (tptp) cc_final: 0.8715 (tppt)
REVERT: A  669 ASP cc_start: 0.7894 (m-30) cc_final: 0.7579 (m-30)
REVERT: B  121 ILE cc_start: 0.9597 (mm) cc_final: 0.9337 (pt)
REVERT: B  132 ILE cc_start: 0.9119 (pt) cc_final: 0.8800 (pt)
REVERT: B  180 MET cc_start: 0.8757 (tpp) cc_final: 0.8423 (mmm)
REVERT: B  299 MET cc_start: 0.9123 (mmp) cc_final: 0.8141 (tmm)
REVERT: B  357 MET cc_start: 0.9042 (tpt) cc_final: 0.8436 (tpp)
REVERT: B  435 LEU cc_start: 0.9265 (mm) cc_final: 0.8977 (mm)
REVERT: B  448 LEU cc_start: 0.9477 (tp) cc_final: 0.9248 (tp)
REVERT: B  451 MET cc_start: 0.8696 (mmp) cc_final: 0.8465 (tpp)
REVERT: B  482 LEU cc_start: 0.9004 (mt) cc_final: 0.8639 (tt)
REVERT: B  633 MET cc_start: 0.8699 (tpt) cc_final: 0.8131 (tpp)
REVERT: B  665 LYS cc_start: 0.9135 (tptp) cc_final: 0.8832 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.0875
  time to fit residues: 22.4426
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  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 56 optimal weight:    5.9990
   chunk 38 optimal weight:   40.0000
   chunk 68 optimal weight:    6.9990
   chunk 81 optimal weight:   50.0000
   chunk 33 optimal weight:    6.9990
   chunk 16 optimal weight:   30.0000
   chunk 43 optimal weight:   10.0000
   chunk 25 optimal weight:   50.0000
   chunk 2 optimal weight:   40.0000
   chunk 58 optimal weight:    0.0170
   overall best weight:    6.0028

-------------------------------------------------------------------------------
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 504 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.080720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.057681 restraints weight = 51046.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.059642 restraints weight = 26990.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.060909 restraints weight = 17978.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.061738 restraints weight = 13750.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.062182 restraints weight = 11615.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10688  Z= 0.141
  Angle     :  0.522   6.485  14532  Z= 0.265
  Chirality :  0.043   0.141   1728
  Planarity :  0.004   0.032   1808
  Dihedral  :  3.331  15.294   1456
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.09 (0.24), residues: 1352
  helix:  2.07 (0.18), residues: 910
  sheet:  3.39 (0.91), residues: 38
  loop : -0.40 (0.34), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 236 
 TYR   0.017   0.001   TYR A 552 
 PHE   0.014   0.001   PHE A 269 
 TRP   0.006   0.001   TRP A  70 
 HIS   0.006   0.001   HIS B  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10688)
  covalent geometry    : angle       0.52172 (14532)
  hydrogen bonds       : bond        0.03260 (  656)
  hydrogen bonds       : angle       3.74703 ( 1902)

*********************** 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
  168 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.427 
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: 0.9012 (pt) cc_final: 0.8611 (pt)
REVERT: A  151 LEU cc_start: 0.9303 (mm) cc_final: 0.9062 (mt)
REVERT: A  253 ASN cc_start: 0.9056 (m-40) cc_final: 0.8814 (p0)
REVERT: A  299 MET cc_start: 0.9090 (mmp) cc_final: 0.8080 (tmm)
REVERT: A  357 MET cc_start: 0.9057 (tpt) cc_final: 0.8646 (tpp)
REVERT: A  435 LEU cc_start: 0.9323 (mm) cc_final: 0.8982 (mm)
REVERT: A  440 LEU cc_start: 0.9531 (mm) cc_final: 0.8963 (tp)
REVERT: A  451 MET cc_start: 0.8721 (mmp) cc_final: 0.8362 (tpp)
REVERT: A  452 PHE cc_start: 0.8724 (m-10) cc_final: 0.8242 (t80)
REVERT: A  633 MET cc_start: 0.8619 (tpt) cc_final: 0.8158 (tpp)
REVERT: A  665 LYS cc_start: 0.9091 (tptp) cc_final: 0.8725 (tppt)
REVERT: A  669 ASP cc_start: 0.7929 (m-30) cc_final: 0.7554 (m-30)
REVERT: B  132 ILE cc_start: 0.9161 (pt) cc_final: 0.8856 (pt)
REVERT: B  180 MET cc_start: 0.8792 (tpp) cc_final: 0.8438 (mmm)
REVERT: B  299 MET cc_start: 0.9152 (mmp) cc_final: 0.8207 (tmm)
REVERT: B  357 MET cc_start: 0.9068 (tpt) cc_final: 0.8678 (tpp)
REVERT: B  435 LEU cc_start: 0.9289 (mm) cc_final: 0.8954 (mm)
REVERT: B  440 LEU cc_start: 0.9564 (mm) cc_final: 0.9042 (tp)
REVERT: B  451 MET cc_start: 0.8709 (mmp) cc_final: 0.8334 (tpp)
REVERT: B  452 PHE cc_start: 0.8802 (m-10) cc_final: 0.8265 (t80)
REVERT: B  482 LEU cc_start: 0.9068 (mt) cc_final: 0.8668 (tt)
REVERT: B  633 MET cc_start: 0.8747 (tpt) cc_final: 0.8201 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0898
  time to fit residues: 22.7338
Evaluate side-chains
  124 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 65 optimal weight:    9.9990
   chunk 111 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 131 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 66 optimal weight:    9.9990
   chunk 132 optimal weight:    3.9990
   chunk 87 optimal weight:    0.3980
   chunk 38 optimal weight:   30.0000
   chunk 62 optimal weight:   20.0000
   chunk 78 optimal weight:    5.9990
   overall best weight:    4.6788

-------------------------------------------------------------------------------
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 = 0.3614 r_free = 0.3614 target = 0.079921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.057394 restraints weight = 52084.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.059376 restraints weight = 27298.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.060682 restraints weight = 17991.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.061474 restraints weight = 13674.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.061991 restraints weight = 11527.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10688  Z= 0.127
  Angle     :  0.526   6.405  14532  Z= 0.264
  Chirality :  0.043   0.156   1728
  Planarity :  0.004   0.036   1808
  Dihedral  :  3.406  18.170   1456
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.14 (0.24), residues: 1352
  helix:  2.12 (0.18), residues: 910
  sheet:  3.28 (0.91), residues: 38
  loop : -0.39 (0.34), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 716 
 TYR   0.016   0.001   TYR A 552 
 PHE   0.025   0.001   PHE B 351 
 TRP   0.007   0.001   TRP B  70 
 HIS   0.005   0.001   HIS A  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (10688)
  covalent geometry    : angle       0.52645 (14532)
  hydrogen bonds       : bond        0.03202 (  656)
  hydrogen bonds       : angle       3.71445 ( 1902)

*********************** 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  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8985 (pt) cc_final: 0.8535 (pt)
REVERT: A  228 TYR cc_start: 0.7716 (m-80) cc_final: 0.7495 (m-80)
REVERT: A  253 ASN cc_start: 0.9070 (m-40) cc_final: 0.8815 (p0)
REVERT: A  299 MET cc_start: 0.9092 (mmp) cc_final: 0.8098 (tmm)
REVERT: A  357 MET cc_start: 0.9079 (tpt) cc_final: 0.8489 (tpp)
REVERT: A  435 LEU cc_start: 0.9297 (mm) cc_final: 0.9036 (mm)
REVERT: A  440 LEU cc_start: 0.9556 (mm) cc_final: 0.8973 (tp)
REVERT: A  446 VAL cc_start: 0.9178 (t) cc_final: 0.8934 (m)
REVERT: A  448 LEU cc_start: 0.9525 (tt) cc_final: 0.9134 (tt)
REVERT: A  452 PHE cc_start: 0.8948 (m-10) cc_final: 0.8227 (t80)
REVERT: A  509 LYS cc_start: 0.8570 (mttt) cc_final: 0.8131 (mmmt)
REVERT: A  633 MET cc_start: 0.8553 (tpt) cc_final: 0.8099 (tpp)
REVERT: A  665 LYS cc_start: 0.9097 (tptp) cc_final: 0.8699 (tppt)
REVERT: A  669 ASP cc_start: 0.7929 (m-30) cc_final: 0.7515 (m-30)
REVERT: B  132 ILE cc_start: 0.9136 (pt) cc_final: 0.8779 (pt)
REVERT: B  180 MET cc_start: 0.8791 (tpp) cc_final: 0.8459 (mmm)
REVERT: B  253 ASN cc_start: 0.9042 (m-40) cc_final: 0.8803 (p0)
REVERT: B  299 MET cc_start: 0.9145 (mmp) cc_final: 0.8200 (tmm)
REVERT: B  357 MET cc_start: 0.9070 (tpt) cc_final: 0.8517 (tpp)
REVERT: B  435 LEU cc_start: 0.9262 (mm) cc_final: 0.9032 (mm)
REVERT: B  452 PHE cc_start: 0.8867 (m-10) cc_final: 0.8210 (t80)
REVERT: B  482 LEU cc_start: 0.9078 (mt) cc_final: 0.8673 (tt)
REVERT: B  633 MET cc_start: 0.8695 (tpt) cc_final: 0.8188 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0901
  time to fit residues: 22.7446
Evaluate side-chains
  129 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 65 optimal weight:    9.9990
   chunk 37 optimal weight:    8.9990
   chunk 34 optimal weight:    9.9990
   chunk 62 optimal weight:   20.0000
   chunk 86 optimal weight:    6.9990
   chunk 23 optimal weight:   20.0000
   chunk 61 optimal weight:    2.9990
   chunk 80 optimal weight:   40.0000
   chunk 15 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    5.5990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.078391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.055715 restraints weight = 52868.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.057668 restraints weight = 27827.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.058933 restraints weight = 18389.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.059759 restraints weight = 14062.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.060256 restraints weight = 11843.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.4168

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= 0.137
  Angle     :  0.546   6.431  14532  Z= 0.273
  Chirality :  0.044   0.187   1728
  Planarity :  0.004   0.038   1808
  Dihedral  :  3.478  17.967   1456
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.23 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.24), residues: 1352
  helix:  2.08 (0.18), residues: 908
  sheet:  3.18 (0.92), residues: 38
  loop : -0.45 (0.34), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 691 
 TYR   0.022   0.001   TYR A 552 
 PHE   0.025   0.001   PHE A 452 
 TRP   0.008   0.001   TRP B 699 
 HIS   0.006   0.001   HIS A  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10688)
  covalent geometry    : angle       0.54613 (14532)
  hydrogen bonds       : bond        0.03249 (  656)
  hydrogen bonds       : angle       3.75018 ( 1902)

*********************** 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
  173 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 172
  time to evaluate  : 0.439 
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: 0.8951 (pt) cc_final: 0.8543 (pt)
REVERT: A  228 TYR cc_start: 0.7572 (m-80) cc_final: 0.7244 (m-80)
REVERT: A  253 ASN cc_start: 0.9087 (m-40) cc_final: 0.8827 (p0)
REVERT: A  299 MET cc_start: 0.9124 (mmp) cc_final: 0.8166 (tmm)
REVERT: A  357 MET cc_start: 0.9030 (tpt) cc_final: 0.8621 (tpp)
REVERT: A  435 LEU cc_start: 0.9308 (mm) cc_final: 0.9025 (mm)
REVERT: A  448 LEU cc_start: 0.9562 (tt) cc_final: 0.9280 (tt)
REVERT: A  451 MET cc_start: 0.8132 (tpp) cc_final: 0.7889 (tpp)
REVERT: A  452 PHE cc_start: 0.8920 (m-10) cc_final: 0.8244 (t80)
REVERT: A  484 LEU cc_start: 0.8636 (mt) cc_final: 0.7852 (tt)
REVERT: A  633 MET cc_start: 0.8565 (tpt) cc_final: 0.8141 (tpp)
REVERT: A  665 LYS cc_start: 0.9117 (tptp) cc_final: 0.8715 (tppt)
REVERT: A  669 ASP cc_start: 0.7929 (m-30) cc_final: 0.7502 (m-30)
REVERT: B  132 ILE cc_start: 0.9136 (pt) cc_final: 0.8826 (pt)
REVERT: B  180 MET cc_start: 0.8775 (tpp) cc_final: 0.8453 (mmm)
REVERT: B  228 TYR cc_start: 0.7691 (m-80) cc_final: 0.7342 (m-80)
REVERT: B  253 ASN cc_start: 0.9041 (m-40) cc_final: 0.8785 (p0)
REVERT: B  299 MET cc_start: 0.9169 (mmp) cc_final: 0.8258 (tmm)
REVERT: B  357 MET cc_start: 0.9030 (tpt) cc_final: 0.8683 (tpp)
REVERT: B  435 LEU cc_start: 0.9264 (mm) cc_final: 0.8983 (mm)
REVERT: B  451 MET cc_start: 0.8106 (tpp) cc_final: 0.7840 (tpp)
REVERT: B  452 PHE cc_start: 0.8861 (m-10) cc_final: 0.8230 (t80)
REVERT: B  509 LYS cc_start: 0.8576 (mttt) cc_final: 0.8331 (mtpt)
REVERT: B  633 MET cc_start: 0.8699 (tpt) cc_final: 0.8203 (tpp)
REVERT: B  665 LYS cc_start: 0.9065 (tppt) cc_final: 0.8709 (tppt)
  outliers start: 1
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0867
  time to fit residues: 22.4648
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  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 110 optimal weight:    7.9990
   chunk 89 optimal weight:   20.0000
   chunk 133 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 47 optimal weight:    7.9990
   chunk 10 optimal weight:   20.0000
   chunk 98 optimal weight:   20.0000
   chunk 119 optimal weight:    0.9990
   chunk 6 optimal weight:    8.9990
   chunk 83 optimal weight:    0.1980
   chunk 67 optimal weight:   10.0000
   overall best weight:    4.8388

-------------------------------------------------------------------------------
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 = 0.3577 r_free = 0.3577 target = 0.078290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.055879 restraints weight = 51856.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.057795 restraints weight = 27346.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.059082 restraints weight = 18124.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.059896 restraints weight = 13814.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.060336 restraints weight = 11637.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.4358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10688  Z= 0.122
  Angle     :  0.515   6.897  14532  Z= 0.257
  Chirality :  0.043   0.165   1728
  Planarity :  0.004   0.037   1808
  Dihedral  :  3.472  17.996   1456
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.24), residues: 1352
  helix:  2.13 (0.18), residues: 908
  sheet:  3.04 (0.90), residues: 38
  loop : -0.32 (0.34), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 716 
 TYR   0.020   0.001   TYR A 552 
 PHE   0.011   0.001   PHE A 452 
 TRP   0.007   0.001   TRP A 699 
 HIS   0.004   0.001   HIS B  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (10688)
  covalent geometry    : angle       0.51507 (14532)
  hydrogen bonds       : bond        0.03115 (  656)
  hydrogen bonds       : angle       3.68850 ( 1902)

*********************** 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
  170 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8930 (pt) cc_final: 0.8461 (pt)
REVERT: A  253 ASN cc_start: 0.9107 (m-40) cc_final: 0.8858 (p0)
REVERT: A  299 MET cc_start: 0.9127 (mmp) cc_final: 0.8171 (tmm)
REVERT: A  357 MET cc_start: 0.9052 (tpt) cc_final: 0.8459 (tpp)
REVERT: A  435 LEU cc_start: 0.9301 (mm) cc_final: 0.8995 (mm)
REVERT: A  440 LEU cc_start: 0.9526 (mm) cc_final: 0.8949 (tp)
REVERT: A  448 LEU cc_start: 0.9590 (tt) cc_final: 0.9262 (tt)
REVERT: A  451 MET cc_start: 0.8093 (tpp) cc_final: 0.7738 (tpp)
REVERT: A  452 PHE cc_start: 0.8973 (m-10) cc_final: 0.8313 (t80)
REVERT: A  484 LEU cc_start: 0.8610 (mt) cc_final: 0.8022 (tt)
REVERT: A  633 MET cc_start: 0.8529 (tpt) cc_final: 0.8122 (tpp)
REVERT: A  665 LYS cc_start: 0.9132 (tptp) cc_final: 0.8905 (tppt)
REVERT: B  132 ILE cc_start: 0.9088 (pt) cc_final: 0.8733 (pt)
REVERT: B  180 MET cc_start: 0.8749 (tpp) cc_final: 0.8385 (mmm)
REVERT: B  253 ASN cc_start: 0.9044 (m-40) cc_final: 0.8797 (p0)
REVERT: B  299 MET cc_start: 0.9177 (mmp) cc_final: 0.8302 (tmm)
REVERT: B  357 MET cc_start: 0.9108 (tpt) cc_final: 0.8524 (tpp)
REVERT: B  435 LEU cc_start: 0.9264 (mm) cc_final: 0.8969 (mm)
REVERT: B  451 MET cc_start: 0.8106 (tpp) cc_final: 0.7692 (tpp)
REVERT: B  488 LEU cc_start: 0.8884 (tt) cc_final: 0.8679 (tp)
REVERT: B  509 LYS cc_start: 0.8558 (mttt) cc_final: 0.8233 (mmmt)
REVERT: B  633 MET cc_start: 0.8669 (tpt) cc_final: 0.8190 (tpp)
REVERT: B  665 LYS cc_start: 0.9082 (tppt) cc_final: 0.8700 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.0775
  time to fit residues: 19.7047
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  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    6.9990
   chunk 120 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   chunk 78 optimal weight:    0.2980
   chunk 97 optimal weight:   20.0000
   chunk 99 optimal weight:    0.0770
   chunk 29 optimal weight:   20.0000
   chunk 58 optimal weight:    6.9990
   chunk 130 optimal weight:   20.0000
   chunk 63 optimal weight:    6.9990
   overall best weight:    1.7740

-------------------------------------------------------------------------------
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 454 GLN
B 454 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.079398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.056806 restraints weight = 51570.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.058816 restraints weight = 27174.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.060089 restraints weight = 17921.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.060944 restraints weight = 13694.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.061423 restraints weight = 11530.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.4479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.056  10688  Z= 0.102
  Angle     :  0.537   7.517  14532  Z= 0.262
  Chirality :  0.043   0.152   1728
  Planarity :  0.004   0.038   1808
  Dihedral  :  3.455  17.878   1456
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.25), residues: 1352
  helix:  2.10 (0.18), residues: 902
  sheet:  3.17 (0.90), residues: 38
  loop : -0.31 (0.34), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 691 
 TYR   0.018   0.001   TYR A 552 
 PHE   0.022   0.001   PHE A 452 
 TRP   0.007   0.001   TRP B  70 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (10688)
  covalent geometry    : angle       0.53667 (14532)
  hydrogen bonds       : bond        0.03052 (  656)
  hydrogen bonds       : angle       3.67813 ( 1902)

*********************** 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
  166 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8892 (pt) cc_final: 0.8406 (pt)
REVERT: A  253 ASN cc_start: 0.9121 (m-40) cc_final: 0.8844 (p0)
REVERT: A  299 MET cc_start: 0.9136 (mmp) cc_final: 0.8185 (tmm)
REVERT: A  357 MET cc_start: 0.8986 (tpt) cc_final: 0.8551 (tpp)
REVERT: A  440 LEU cc_start: 0.9526 (mm) cc_final: 0.8950 (tp)
REVERT: A  448 LEU cc_start: 0.9545 (tt) cc_final: 0.9326 (tt)
REVERT: A  452 PHE cc_start: 0.8892 (m-10) cc_final: 0.8217 (t80)
REVERT: A  484 LEU cc_start: 0.8609 (mt) cc_final: 0.7939 (tt)
REVERT: A  509 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7993 (mmmt)
REVERT: A  633 MET cc_start: 0.8525 (tpt) cc_final: 0.8140 (tpp)
REVERT: A  665 LYS cc_start: 0.9202 (tptp) cc_final: 0.8685 (tppt)
REVERT: A  669 ASP cc_start: 0.7915 (m-30) cc_final: 0.7265 (m-30)
REVERT: B  132 ILE cc_start: 0.9034 (pt) cc_final: 0.8643 (pt)
REVERT: B  180 MET cc_start: 0.8887 (tpp) cc_final: 0.8559 (mmm)
REVERT: B  253 ASN cc_start: 0.9044 (m-40) cc_final: 0.8760 (p0)
REVERT: B  276 LYS cc_start: 0.8416 (tttt) cc_final: 0.7973 (ptmt)
REVERT: B  299 MET cc_start: 0.9185 (mmp) cc_final: 0.8286 (tmm)
REVERT: B  357 MET cc_start: 0.9034 (tpt) cc_final: 0.8645 (tpp)
REVERT: B  509 LYS cc_start: 0.8492 (mttt) cc_final: 0.8040 (mmmt)
REVERT: B  633 MET cc_start: 0.8649 (tpt) cc_final: 0.8425 (tpp)
REVERT: B  665 LYS cc_start: 0.9092 (tppt) cc_final: 0.8715 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0813
  time to fit residues: 20.3450
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  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 99 optimal weight:    0.0170
   chunk 62 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 118 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 36 optimal weight:   40.0000
   chunk 12 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   overall best weight:    3.3824

-------------------------------------------------------------------------------
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 = 0.3591 r_free = 0.3591 target = 0.079248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.056619 restraints weight = 52091.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.058630 restraints weight = 27137.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.059903 restraints weight = 17773.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.060757 restraints weight = 13550.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.061133 restraints weight = 11363.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.4558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  10688  Z= 0.110
  Angle     :  0.533   7.332  14532  Z= 0.262
  Chirality :  0.043   0.153   1728
  Planarity :  0.004   0.038   1808
  Dihedral  :  3.475  17.482   1456
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.25), residues: 1352
  helix:  2.13 (0.18), residues: 902
  sheet:  3.16 (0.90), residues: 38
  loop : -0.31 (0.34), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 236 
 TYR   0.017   0.001   TYR A 552 
 PHE   0.030   0.001   PHE B 351 
 TRP   0.007   0.001   TRP B  70 
 HIS   0.005   0.001   HIS A  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (10688)
  covalent geometry    : angle       0.53314 (14532)
  hydrogen bonds       : bond        0.03046 (  656)
  hydrogen bonds       : angle       3.68999 ( 1902)

*********************** 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
  164 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8896 (pt) cc_final: 0.8416 (pt)
REVERT: A  253 ASN cc_start: 0.9114 (m-40) cc_final: 0.8851 (p0)
REVERT: A  299 MET cc_start: 0.9141 (mmp) cc_final: 0.8188 (tmm)
REVERT: A  357 MET cc_start: 0.9064 (tpt) cc_final: 0.8443 (tpp)
REVERT: A  484 LEU cc_start: 0.8584 (mt) cc_final: 0.7987 (tt)
REVERT: A  509 LYS cc_start: 0.8255 (mtpt) cc_final: 0.8055 (mmmt)
REVERT: A  633 MET cc_start: 0.8536 (tpt) cc_final: 0.8142 (tpp)
REVERT: A  665 LYS cc_start: 0.9164 (tptp) cc_final: 0.8963 (tppt)
REVERT: B  132 ILE cc_start: 0.9024 (pt) cc_final: 0.8616 (pt)
REVERT: B  180 MET cc_start: 0.8875 (tpp) cc_final: 0.8426 (mmm)
REVERT: B  253 ASN cc_start: 0.9048 (m-40) cc_final: 0.8786 (p0)
REVERT: B  276 LYS cc_start: 0.8433 (tttt) cc_final: 0.8031 (ptmt)
REVERT: B  299 MET cc_start: 0.9184 (mmp) cc_final: 0.8289 (tmm)
REVERT: B  357 MET cc_start: 0.9085 (tpt) cc_final: 0.8592 (tpp)
REVERT: B  451 MET cc_start: 0.8515 (tpp) cc_final: 0.8298 (tmm)
REVERT: B  509 LYS cc_start: 0.8525 (mttt) cc_final: 0.8106 (mmmt)
REVERT: B  633 MET cc_start: 0.8660 (tpt) cc_final: 0.8196 (tpp)
REVERT: B  665 LYS cc_start: 0.9074 (tppt) cc_final: 0.8735 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0882
  time to fit residues: 21.4154
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  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 26 optimal weight:   50.0000
   chunk 11 optimal weight:   40.0000
   chunk 111 optimal weight:    5.9990
   chunk 1 optimal weight:   20.0000
   chunk 76 optimal weight:   10.0000
   chunk 32 optimal weight:    0.7980
   chunk 125 optimal weight:   20.0000
   chunk 78 optimal weight:    8.9990
   chunk 29 optimal weight:    8.9990
   chunk 48 optimal weight:   10.0000
   chunk 79 optimal weight:   30.0000
   overall best weight:    6.9590

-------------------------------------------------------------------------------
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**
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 = 0.077432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.054771 restraints weight = 52056.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.056655 restraints weight = 27603.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.057878 restraints weight = 18368.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.058639 restraints weight = 14147.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.059055 restraints weight = 12032.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.4900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10688  Z= 0.158
  Angle     :  0.580   8.335  14532  Z= 0.288
  Chirality :  0.044   0.159   1728
  Planarity :  0.004   0.038   1808
  Dihedral  :  3.663  17.921   1456
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.25), residues: 1352
  helix:  2.02 (0.18), residues: 902
  sheet:  3.03 (0.91), residues: 38
  loop : -0.33 (0.34), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 236 
 TYR   0.018   0.001   TYR A 552 
 PHE   0.035   0.001   PHE B 351 
 TRP   0.008   0.001   TRP A 699 
 HIS   0.005   0.001   HIS A  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (10688)
  covalent geometry    : angle       0.58006 (14532)
  hydrogen bonds       : bond        0.03312 (  656)
  hydrogen bonds       : angle       3.83950 ( 1902)

********************** 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
  154 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ILE cc_start: 0.8922 (pt) cc_final: 0.8552 (pt)
REVERT: A  253 ASN cc_start: 0.9100 (m-40) cc_final: 0.8853 (p0)
REVERT: A  299 MET cc_start: 0.9163 (mmp) cc_final: 0.8212 (tmm)
REVERT: A  357 MET cc_start: 0.9042 (tpt) cc_final: 0.8636 (tpp)
REVERT: A  484 LEU cc_start: 0.8627 (mt) cc_final: 0.7973 (tt)
REVERT: A  633 MET cc_start: 0.8559 (tpt) cc_final: 0.8162 (tpp)
REVERT: A  665 LYS cc_start: 0.9145 (tptp) cc_final: 0.8931 (tppt)
REVERT: B  132 ILE cc_start: 0.9060 (pt) cc_final: 0.8743 (pt)
REVERT: B  180 MET cc_start: 0.8902 (tpp) cc_final: 0.8490 (mmm)
REVERT: B  253 ASN cc_start: 0.9066 (m-40) cc_final: 0.8798 (p0)
REVERT: B  299 MET cc_start: 0.9188 (mmp) cc_final: 0.8305 (tmm)
REVERT: B  357 MET cc_start: 0.9136 (tpt) cc_final: 0.8816 (tpp)
REVERT: B  509 LYS cc_start: 0.8602 (mttt) cc_final: 0.8213 (mmmt)
REVERT: B  633 MET cc_start: 0.8676 (tpt) cc_final: 0.8189 (tpp)
REVERT: B  665 LYS cc_start: 0.9069 (tppt) cc_final: 0.8690 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0847
  time to fit residues: 19.7049
Evaluate side-chains
  122 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 37 optimal weight:   20.0000
   chunk 36 optimal weight:    7.9990
   chunk 116 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 89 optimal weight:   10.0000
   chunk 122 optimal weight:    0.9990
   chunk 16 optimal weight:   40.0000
   chunk 35 optimal weight:   20.0000
   chunk 12 optimal weight:   30.0000
   chunk 118 optimal weight:   20.0000
   overall best weight:    4.5988

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.078103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.055370 restraints weight = 52334.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.057299 restraints weight = 27488.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.058550 restraints weight = 18233.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.059344 restraints weight = 13980.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.059852 restraints weight = 11852.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.4974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10688  Z= 0.124
  Angle     :  0.555   7.578  14532  Z= 0.273
  Chirality :  0.043   0.148   1728
  Planarity :  0.004   0.037   1808
  Dihedral  :  3.634  19.596   1456
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.25), residues: 1352
  helix:  2.04 (0.18), residues: 902
  sheet:  2.94 (0.89), residues: 38
  loop : -0.28 (0.34), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 211 
 TYR   0.017   0.001   TYR A 552 
 PHE   0.034   0.001   PHE B 351 
 TRP   0.027   0.002   TRP B 699 
 HIS   0.010   0.001   HIS B  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10688)
  covalent geometry    : angle       0.55496 (14532)
  hydrogen bonds       : bond        0.03163 (  656)
  hydrogen bonds       : angle       3.76471 ( 1902)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1785.75 seconds
wall clock time: 31 minutes 36.87 seconds (1896.87 seconds total)