Starting phenix.real_space_refine
on Fri Feb 14 18:14:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lh2_23334/02_2025/7lh2_23334.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lh2_23334/02_2025/7lh2_23334.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lh2_23334/02_2025/7lh2_23334.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lh2_23334/02_2025/7lh2_23334.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lh2_23334/02_2025/7lh2_23334.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lh2_23334/02_2025/7lh2_23334.cif"
  }
  resolution = 3.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.025
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    6930      2.51       5
     N    1690      2.21       5
     O    1860      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10528
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 680, 5226
          Classifications: {'peptide': 680}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 34, 'TRANS': 645}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "B"
      Number of atoms: 5226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 680, 5226
          Classifications: {'peptide': 680}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 34, 'TRANS': 645}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {'CLR': 1, 'SAL': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {'CLR': 1, 'SAL': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.49, per 1000 atoms: 0.62
  Number of scatterers: 10528
  At special positions: 0
  Unit cell: (102.16, 120.379, 113.872, 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    1860      8.00
     N    1690      7.00
     C    6930      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.49
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 5 sheets defined
      69.6% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 30
    Processing helix  chain 'A' and resid 43 through 48
      removed outlier: 3.592A  pdb=" N   LYS A  47 " --> pdb=" O   ALA A  43 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   GLN A  48 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 43 through 48'
    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: 5.451A  pdb=" N   LEU A  81 " --> pdb=" O   LYS A  77 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   GLY A  82 " --> pdb=" O   GLU A  78 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   LEU A  93 " --> pdb=" O   SER A  89 " (cutoff:3.500A)
      Proline residue:  A  96  - end of helix
    Processing helix  chain 'A' and resid 109 through 115
      removed outlier: 3.768A  pdb=" N   LEU A 113 " --> pdb=" O   PRO A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 127
      removed outlier: 3.664A  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: 3.982A  pdb=" N   PHE A 200 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA A 202 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
      removed outlier: 3.828A  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: 3.614A  pdb=" N   PHE A 295 " --> pdb=" O   PRO A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 313
      removed outlier: 3.845A  pdb=" N   TYR A 313 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 366
      removed outlier: 6.494A  pdb=" N   VAL A 341 " --> pdb=" O   HIS A 337 " (cutoff:3.500A)
      removed outlier: 5.844A  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 427
    Processing helix  chain 'A' and resid 436 through 448
      removed outlier: 3.783A  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: 3.549A  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: 3.866A  pdb=" N   LEU A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ILE A 489 " --> pdb=" O   ASP A 485 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   VAL A 499 " --> pdb=" O   ALA A 495 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ILE A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 560
      removed outlier: 3.670A  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: 3.747A  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 695 through 702
      removed outlier: 3.928A  pdb=" N   GLU A 700 " --> pdb=" O   ALA A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 725
      removed outlier: 4.045A  pdb=" N   SER A 725 " --> pdb=" O   GLU A 721 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 30
    Processing helix  chain 'B' and resid 43 through 48
      removed outlier: 3.592A  pdb=" N   LYS B  47 " --> pdb=" O   ALA B  43 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   GLN B  48 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 43 through 48'
    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: 5.451A  pdb=" N   LEU B  81 " --> pdb=" O   LYS B  77 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   GLY B  82 " --> pdb=" O   GLU B  78 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   LEU B  93 " --> pdb=" O   SER B  89 " (cutoff:3.500A)
      Proline residue:  B  96  - end of helix
    Processing helix  chain 'B' and resid 109 through 115
      removed outlier: 3.769A  pdb=" N   LEU B 113 " --> pdb=" O   PRO B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 127
      removed outlier: 3.665A  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: 3.982A  pdb=" N   PHE B 200 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA B 202 " --> pdb=" O   GLY B 199 " (cutoff:3.500A)
      removed outlier: 3.828A  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: 3.614A  pdb=" N   PHE B 295 " --> pdb=" O   PRO B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 313
      removed outlier: 3.846A  pdb=" N   TYR B 313 " --> pdb=" O   LEU B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 366
      removed outlier: 6.493A  pdb=" N   VAL B 341 " --> pdb=" O   HIS B 337 " (cutoff:3.500A)
      removed outlier: 5.844A  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 427
    Processing helix  chain 'B' and resid 436 through 448
      removed outlier: 3.783A  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: 3.548A  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: 3.866A  pdb=" N   LEU B 488 " --> pdb=" O   LEU B 484 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ILE B 489 " --> pdb=" O   ASP B 485 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   VAL B 499 " --> pdb=" O   ALA B 495 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ILE B 500 " --> pdb=" O   LEU B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 548 through 560
      removed outlier: 3.670A  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: 3.747A  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 695 through 702
      removed outlier: 3.928A  pdb=" N   GLU B 700 " --> pdb=" O   ALA B 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 725
      removed outlier: 4.044A  pdb=" N   SER B 725 " --> pdb=" O   GLU B 721 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20
    Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 135
      removed outlier: 3.587A  pdb=" N   SER A 394 " --> pdb=" O   GLY A 135 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522
      removed outlier: 4.891A  pdb=" N   ILE A 537 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
      removed outlier: 8.337A  pdb=" N   LYS A 513 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
      removed outlier: 12.029A  pdb=" N   ILE A 535 " --> pdb=" O   LYS A 513 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   LYS A 536 " --> pdb=" O   ILE A 643 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   ASP A 645 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   PHE A 538 " --> pdb=" O   ASP A 645 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   VAL A 642 " --> pdb=" O   TYR A 675 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   ALA A 677 " --> pdb=" O   VAL A 642 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   LEU A 644 " --> pdb=" O   ALA A 677 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 135
      removed outlier: 3.588A  pdb=" N   SER B 394 " --> pdb=" O   GLY B 135 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522
      removed outlier: 4.891A  pdb=" N   ILE B 537 " --> pdb=" O   LEU B 511 " (cutoff:3.500A)
      removed outlier: 8.337A  pdb=" N   LYS B 513 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 12.029A  pdb=" N   ILE B 535 " --> pdb=" O   LYS B 513 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   LYS B 536 " --> pdb=" O   ILE B 643 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   ASP B 645 " --> pdb=" O   LYS B 536 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   PHE B 538 " --> pdb=" O   ASP B 645 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   VAL B 642 " --> pdb=" O   TYR B 675 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   ALA B 677 " --> pdb=" O   VAL B 642 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   LEU B 644 " --> pdb=" O   ALA B 677 " (cutoff:3.500A)

    646 hydrogen bonds defined for protein.
    1878 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.25

  Time building geometry restraints manager: 2.92 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: 3242
        1.34 -     1.46: 2346
        1.46 -     1.58: 5104
        1.58 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 10770
  Sorted by residual:
  bond pdb=" C1  SAL A 801 "
       pdb=" C2  SAL A 801 "
    ideal  model  delta    sigma   weight residual
    1.409  1.484 -0.075 2.00e-02 2.50e+03 1.39e+01
  bond pdb=" C1  SAL B 801 "
       pdb=" C2  SAL B 801 "
    ideal  model  delta    sigma   weight residual
    1.409  1.484 -0.075 2.00e-02 2.50e+03 1.39e+01
  bond pdb=" N   VAL B 402 "
       pdb=" CA  VAL B 402 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.033 1.19e-02 7.06e+03 7.49e+00
  bond pdb=" N   SER B 398 "
       pdb=" CA  SER B 398 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.19e-02 7.06e+03 6.66e+00
  bond pdb=" N   GLN B 403 "
       pdb=" CA  GLN B 403 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.83e+00
  ... (remaining 10765 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 14416
        1.90 -     3.80: 198
        3.80 -     5.70: 36
        5.70 -     7.59: 2
        7.59 -     9.49: 2
  Bond angle restraints: 14654
  Sorted by residual:
  angle pdb=" O   VAL B 402 "
        pdb=" C   VAL B 402 "
        pdb=" N   GLN B 403 "
      ideal   model   delta    sigma   weight residual
     121.87  124.67   -2.80 9.70e-01 1.06e+00 8.32e+00
  angle pdb=" CA  LEU A 448 "
        pdb=" CB  LEU A 448 "
        pdb=" CG  LEU A 448 "
      ideal   model   delta    sigma   weight residual
     116.30  125.79   -9.49 3.50e+00 8.16e-02 7.36e+00
  angle pdb=" CA  LEU B 448 "
        pdb=" CB  LEU B 448 "
        pdb=" CG  LEU B 448 "
      ideal   model   delta    sigma   weight residual
     116.30  125.74   -9.44 3.50e+00 8.16e-02 7.27e+00
  angle pdb=" CA  SER B 398 "
        pdb=" C   SER B 398 "
        pdb=" O   SER B 398 "
      ideal   model   delta    sigma   weight residual
     120.82  118.04    2.78 1.05e+00 9.07e-01 7.00e+00
  angle pdb=" CA  ARG B 399 "
        pdb=" C   ARG B 399 "
        pdb=" O   ARG B 399 "
      ideal   model   delta    sigma   weight residual
     120.55  117.84    2.71 1.06e+00 8.90e-01 6.52e+00
  ... (remaining 14649 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.06: 5809
       16.06 -    32.13: 527
       32.13 -    48.19: 100
       48.19 -    64.25: 22
       64.25 -    80.32: 12
  Dihedral angle restraints: 6470
    sinusoidal: 2546
      harmonic: 3924
  Sorted by residual:
  dihedral pdb=" CA  PHE A  23 "
           pdb=" C   PHE A  23 "
           pdb=" N   SER A  24 "
           pdb=" CA  SER A  24 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.58   19.42     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  PHE B  23 "
           pdb=" C   PHE B  23 "
           pdb=" N   SER B  24 "
           pdb=" CA  SER B  24 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.58   19.42     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  ASP B 686 "
           pdb=" CB  ASP B 686 "
           pdb=" CG  ASP B 686 "
           pdb=" OD1 ASP B 686 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.57   57.57     1      2.00e+01 2.50e-03 1.11e+01
  ... (remaining 6467 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1174
       0.039 -    0.077: 427
       0.077 -    0.116: 123
       0.116 -    0.154: 16
       0.154 -    0.193: 4
  Chirality restraints: 1744
  Sorted by residual:
  chirality pdb=" CG  LEU A 193 "
            pdb=" CB  LEU A 193 "
            pdb=" CD1 LEU A 193 "
            pdb=" CD2 LEU A 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.30e-01
  chirality pdb=" CG  LEU B 193 "
            pdb=" CB  LEU B 193 "
            pdb=" CD1 LEU B 193 "
            pdb=" CD2 LEU B 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.19e-01
  chirality pdb=" CA  VAL B 402 "
            pdb=" N   VAL B 402 "
            pdb=" C   VAL B 402 "
            pdb=" CB  VAL B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.28e-01
  ... (remaining 1741 not shown)

  Planarity restraints: 1812
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 633 "   -0.035 5.00e-02 4.00e+02   5.34e-02 4.57e+00
        pdb=" N   PRO B 634 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 634 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 634 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 633 "    0.035 5.00e-02 4.00e+02   5.33e-02 4.55e+00
        pdb=" N   PRO A 634 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 634 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 634 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 198 "    0.015 2.00e-02 2.50e+03   1.47e-02 3.78e+00
        pdb=" CG  PHE B 198 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 198 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 198 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 198 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 198 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 198 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1809 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 64
        2.60 -     3.18: 9454
        3.18 -     3.75: 16149
        3.75 -     4.33: 21547
        4.33 -     4.90: 36174
  Nonbonded interactions: 83388
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 398 "
            pdb=" O2' SAL A 801 "
     model   vdw
     2.030 3.040
  nonbonded pdb=" OG  SER B  86 "
            pdb=" O   GLN B 403 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" OD2 ASP A  83 "
            pdb=" OG1 THR A 410 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OD2 ASP B  83 "
            pdb=" OG1 THR B 410 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OG1 THR B 503 "
            pdb=" OH  TYR B 545 "
     model   vdw
     2.226 3.040
  ... (remaining 83383 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     26.060
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
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      :  0.003   0.075  10770  Z= 0.198
  Angle     :  0.558   9.493  14654  Z= 0.304
  Chirality :  0.043   0.193   1744
  Planarity :  0.004   0.053   1812
  Dihedral  : 13.017  80.315   3958
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.53 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.24), residues: 1352
  helix:  1.34 (0.18), residues: 894
  sheet:  1.90 (0.69), residues: 52
  loop : -1.07 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 472 
 HIS   0.002   0.001   HIS A  25 
 PHE   0.034   0.001   PHE B 198 
 TYR   0.014   0.001   TYR B 237 
 ARG   0.008   0.001   ARG B 572 

*********************** 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
  148 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 146
  time to evaluate  : 1.276 
Fit side-chains
REVERT: A  545 TYR cc_start: 0.8268 (p90) cc_final: 0.7954 (p90)
  outliers start: 2
  outliers final: 2
  residues processed: 146
  average time/residue: 0.1845
  time to fit residues: 41.2222
Evaluate side-chains
  105 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  453 MET
Chi-restraints excluded: chain B residue  453 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:   10.0000
   chunk 103 optimal weight:    7.9990
   chunk 57 optimal weight:    0.2980
   chunk 35 optimal weight:    9.9990
   chunk 69 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 64 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 123 optimal weight:    6.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 690 ASN
** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 690 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.140280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.114676 restraints weight = 16162.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.11
r_work: 0.3370 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  10770  Z= 0.171
  Angle     :  0.533  11.041  14654  Z= 0.263
  Chirality :  0.042   0.128   1744
  Planarity :  0.004   0.050   1812
  Dihedral  :  4.935  42.852   1594
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  7.67 %
    Favored  : 91.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.24), residues: 1352
  helix:  1.60 (0.18), residues: 896
  sheet:  2.11 (0.70), residues: 52
  loop : -1.03 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 699 
 HIS   0.006   0.001   HIS A 704 
 PHE   0.021   0.001   PHE A 198 
 TYR   0.012   0.001   TYR A 237 
 ARG   0.004   0.000   ARG B 399 

*********************** 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
  138 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 1.227 
Fit side-chains
REVERT: A  198 PHE cc_start: 0.7745 (t80) cc_final: 0.7501 (t80)
REVERT: A  545 TYR cc_start: 0.8589 (p90) cc_final: 0.8146 (p90)
REVERT: A  575 MET cc_start: 0.7648 (tmm) cc_final: 0.7446 (tmm)
REVERT: B  198 PHE cc_start: 0.7324 (t80) cc_final: 0.6889 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 132
  average time/residue: 0.2110
  time to fit residues: 41.3016
Evaluate side-chains
  116 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  486 TYR
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  424 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 90 optimal weight:    0.0050
   chunk 123 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 122 optimal weight:    2.9990
   chunk 107 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 119 optimal weight:    9.9990
   chunk 100 optimal weight:    0.9990
   chunk 63 optimal weight:    7.9990
   chunk 65 optimal weight:    0.5980
   chunk 106 optimal weight:    9.9990
   overall best weight:    1.5200

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.141262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.115540 restraints weight = 16349.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.09
r_work: 0.3385 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10770  Z= 0.149
  Angle     :  0.508  10.027  14654  Z= 0.248
  Chirality :  0.042   0.128   1744
  Planarity :  0.004   0.054   1812
  Dihedral  :  4.263  38.362   1588
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  8.64 %
    Favored  : 89.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.24), residues: 1352
  helix:  1.83 (0.18), residues: 886
  sheet:  2.18 (0.70), residues: 52
  loop : -0.85 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  70 
 HIS   0.003   0.001   HIS A 704 
 PHE   0.015   0.001   PHE A 198 
 TYR   0.015   0.001   TYR A 578 
 ARG   0.005   0.000   ARG B 572 

*********************** 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
  139 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 1.173 
Fit side-chains
   revert: symmetry clash
REVERT: A  575 MET cc_start: 0.7734 (tmm) cc_final: 0.7435 (tmm)
REVERT: B  198 PHE cc_start: 0.7243 (t80) cc_final: 0.6796 (t80)
REVERT: B  694 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6755 (mp0)
  outliers start: 22
  outliers final: 15
  residues processed: 135
  average time/residue: 0.1926
  time to fit residues: 39.9811
Evaluate side-chains
  125 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  453 MET
Chi-restraints excluded: chain A residue  486 TYR
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  398 SER
Chi-restraints excluded: chain B residue  453 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 64 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 112 optimal weight:    0.0470
   chunk 88 optimal weight:    7.9990
   chunk 65 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 125 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   overall best weight:    3.1884

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

Flipped N/Q/H residues before XYZ refinement:
** B 504 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 = 0.3855 r_free = 0.3855 target = 0.137878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.109975 restraints weight = 16357.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 2.41
r_work: 0.3316 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10770  Z= 0.228
  Angle     :  0.532   7.962  14654  Z= 0.263
  Chirality :  0.043   0.126   1744
  Planarity :  0.004   0.055   1812
  Dihedral  :  4.156  34.086   1588
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.73 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.24), residues: 1352
  helix:  1.84 (0.18), residues: 888
  sheet:  2.00 (0.69), residues: 52
  loop : -0.81 (0.33), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  70 
 HIS   0.004   0.001   HIS A 704 
 PHE   0.014   0.001   PHE A 198 
 TYR   0.016   0.001   TYR B 578 
 ARG   0.005   0.000   ARG B 572 

*********************** 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
  134 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 1.230 
Fit side-chains
   revert: symmetry clash
REVERT: A  575 MET cc_start: 0.7746 (tmm) cc_final: 0.7409 (tmm)
REVERT: A  694 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6576 (mp0)
REVERT: B  198 PHE cc_start: 0.7257 (t80) cc_final: 0.6793 (t80)
REVERT: B  227 LYS cc_start: 0.7781 (ptmt) cc_final: 0.7414 (ptpp)
  outliers start: 20
  outliers final: 17
  residues processed: 132
  average time/residue: 0.1988
  time to fit residues: 40.0433
Evaluate side-chains
  125 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  486 TYR
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  398 SER
Chi-restraints excluded: chain B residue  452 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 26 optimal weight:   30.0000
   chunk 51 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 41 optimal weight:    9.9990
   chunk 125 optimal weight:    7.9990
   chunk 94 optimal weight:   30.0000
   chunk 76 optimal weight:    6.9990
   chunk 75 optimal weight:    6.9990
   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 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 504 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 = 0.3801 r_free = 0.3801 target = 0.133723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.107520 restraints weight = 16607.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 2.13
r_work: 0.3272 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040  10770  Z= 0.361
  Angle     :  0.595   7.101  14654  Z= 0.302
  Chirality :  0.045   0.146   1744
  Planarity :  0.004   0.059   1812
  Dihedral  :  4.360  43.875   1588
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.23 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.24), residues: 1352
  helix:  1.56 (0.18), residues: 894
  sheet:  1.68 (0.68), residues: 52
  loop : -0.98 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  70 
 HIS   0.004   0.001   HIS A 704 
 PHE   0.020   0.002   PHE A 198 
 TYR   0.018   0.002   TYR A 545 
 ARG   0.006   0.001   ARG B 572 

*********************** 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
  137 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 1.158 
Fit side-chains
REVERT: A  227 LYS cc_start: 0.7807 (ptmt) cc_final: 0.7468 (ptpt)
REVERT: A  575 MET cc_start: 0.7983 (tmm) cc_final: 0.7588 (tmm)
REVERT: B  198 PHE cc_start: 0.7417 (t80) cc_final: 0.6933 (t80)
REVERT: B  227 LYS cc_start: 0.7756 (ptmt) cc_final: 0.7487 (ptpt)
  outliers start: 24
  outliers final: 19
  residues processed: 133
  average time/residue: 0.2140
  time to fit residues: 42.4081
Evaluate side-chains
  123 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   59 ASN
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  398 SER
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  452 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 83 optimal weight:   20.0000
   chunk 10 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 120 optimal weight:    3.9990
   chunk 26 optimal weight:   30.0000
   chunk 71 optimal weight:    0.0470
   chunk 123 optimal weight:    0.0980
   chunk 42 optimal weight:    9.9990
   chunk 119 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 96 optimal weight:    6.9990
   overall best weight:    1.0282

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 504 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 = 0.3935 r_free = 0.3935 target = 0.141930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.113460 restraints weight = 16344.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.41
r_work: 0.3419 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10770  Z= 0.139
  Angle     :  0.522  10.299  14654  Z= 0.254
  Chirality :  0.042   0.189   1744
  Planarity :  0.004   0.058   1812
  Dihedral  :  4.224  45.554   1588
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 14.64 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.24), residues: 1352
  helix:  1.93 (0.18), residues: 882
  sheet:  1.86 (0.69), residues: 52
  loop : -0.71 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  70 
 HIS   0.002   0.001   HIS A 704 
 PHE   0.014   0.001   PHE A 198 
 TYR   0.010   0.001   TYR A 313 
 ARG   0.004   0.000   ARG B 576 

*********************** 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
  131 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 1.201 
Fit side-chains
REVERT: A   70 TRP cc_start: 0.7948 (p-90) cc_final: 0.7711 (p-90)
REVERT: A  198 PHE cc_start: 0.7640 (t80) cc_final: 0.7409 (t80)
REVERT: A  227 LYS cc_start: 0.7768 (ptmt) cc_final: 0.7414 (ptpt)
REVERT: A  575 MET cc_start: 0.8073 (tmm) cc_final: 0.7685 (tmm)
REVERT: A  694 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6873 (mp0)
REVERT: B  198 PHE cc_start: 0.7375 (t80) cc_final: 0.6852 (t80)
REVERT: B  227 LYS cc_start: 0.7708 (ptmt) cc_final: 0.7422 (ptpt)
REVERT: B  576 ARG cc_start: 0.7738 (ptt-90) cc_final: 0.7484 (mtm-85)
REVERT: B  694 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6916 (mp0)
  outliers start: 15
  outliers final: 15
  residues processed: 126
  average time/residue: 0.1988
  time to fit residues: 37.9574
Evaluate side-chains
  124 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  452 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 93 optimal weight:    9.9990
   chunk 8 optimal weight:    7.9990
   chunk 35 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 83 optimal weight:    8.9990
   chunk 114 optimal weight:    9.9990
   chunk 58 optimal weight:   40.0000
   chunk 16 optimal weight:    2.9990
   chunk 66 optimal weight:    8.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 504 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 = 0.3895 r_free = 0.3895 target = 0.138757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.112649 restraints weight = 16720.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.11
r_work: 0.3386 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10770  Z= 0.248
  Angle     :  0.547   8.275  14654  Z= 0.270
  Chirality :  0.043   0.131   1744
  Planarity :  0.004   0.058   1812
  Dihedral  :  4.331  48.968   1588
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 15.34 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.24), residues: 1352
  helix:  1.93 (0.18), residues: 884
  sheet:  1.71 (0.68), residues: 52
  loop : -0.76 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B  70 
 HIS   0.002   0.001   HIS A 704 
 PHE   0.016   0.001   PHE A 198 
 TYR   0.014   0.001   TYR A 545 
 ARG   0.005   0.000   ARG A 572 

*********************** 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
  125 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 1.236 
Fit side-chains
REVERT: A   70 TRP cc_start: 0.7955 (p-90) cc_final: 0.7700 (p-90)
REVERT: A  227 LYS cc_start: 0.7885 (ptmt) cc_final: 0.7552 (ptpt)
REVERT: A  575 MET cc_start: 0.8044 (tmm) cc_final: 0.7644 (tmm)
REVERT: B  198 PHE cc_start: 0.7438 (t80) cc_final: 0.6921 (t80)
REVERT: B  227 LYS cc_start: 0.7835 (ptmt) cc_final: 0.7583 (ptpt)
  outliers start: 16
  outliers final: 16
  residues processed: 121
  average time/residue: 0.2165
  time to fit residues: 39.1435
Evaluate side-chains
  120 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 1.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  452 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 33 optimal weight:    4.9990
   chunk 82 optimal weight:    0.0570
   chunk 118 optimal weight:    0.9990
   chunk 122 optimal weight:    4.9990
   chunk 105 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 134 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    2.3904

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 504 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 = 0.3920 r_free = 0.3920 target = 0.140609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.114771 restraints weight = 16450.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 2.08
r_work: 0.3416 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10770  Z= 0.187
  Angle     :  0.529   8.717  14654  Z= 0.259
  Chirality :  0.042   0.124   1744
  Planarity :  0.004   0.057   1812
  Dihedral  :  4.358  51.353   1588
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 15.17 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.24), residues: 1352
  helix:  1.96 (0.18), residues: 884
  sheet:  1.82 (0.69), residues: 52
  loop : -0.71 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  70 
 HIS   0.002   0.001   HIS A 220 
 PHE   0.014   0.001   PHE A 198 
 TYR   0.014   0.001   TYR A 237 
 ARG   0.006   0.000   ARG B 576 

*********************** 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
  131 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 1.206 
Fit side-chains
REVERT: A   70 TRP cc_start: 0.7919 (p-90) cc_final: 0.7703 (p-90)
REVERT: A  227 LYS cc_start: 0.7910 (ptmt) cc_final: 0.7571 (ptpt)
REVERT: A  575 MET cc_start: 0.8082 (tmm) cc_final: 0.7678 (tmm)
REVERT: A  694 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6593 (mp0)
REVERT: B  198 PHE cc_start: 0.7415 (t80) cc_final: 0.6875 (t80)
REVERT: B  227 LYS cc_start: 0.7807 (ptmt) cc_final: 0.7558 (ptpt)
REVERT: B  576 ARG cc_start: 0.7688 (ptt-90) cc_final: 0.7386 (mtm-85)
REVERT: B  694 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6906 (mp0)
  outliers start: 20
  outliers final: 17
  residues processed: 127
  average time/residue: 0.2068
  time to fit residues: 39.1455
Evaluate side-chains
  126 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   59 ASN
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  486 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 100 optimal weight:    0.8980
   chunk 22 optimal weight:    0.1980
   chunk 16 optimal weight:    5.9990
   chunk 129 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 118 optimal weight:    0.5980
   chunk 34 optimal weight:    7.9990
   chunk 110 optimal weight:   10.0000
   chunk 131 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 504 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 = 0.3925 r_free = 0.3925 target = 0.141090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.115094 restraints weight = 16631.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 2.11
r_work: 0.3427 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10770  Z= 0.176
  Angle     :  0.521   8.661  14654  Z= 0.256
  Chirality :  0.042   0.124   1744
  Planarity :  0.004   0.056   1812
  Dihedral  :  4.370  53.431   1588
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.26 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.24), residues: 1352
  helix:  1.99 (0.18), residues: 884
  sheet:  1.90 (0.69), residues: 52
  loop : -0.70 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B  70 
 HIS   0.002   0.001   HIS A 220 
 PHE   0.014   0.001   PHE A 198 
 TYR   0.010   0.001   TYR A 545 
 ARG   0.009   0.000   ARG A 576 

*********************** 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
  127 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 1.002 
Fit side-chains
REVERT: A  227 LYS cc_start: 0.7879 (ptmt) cc_final: 0.7510 (ptpp)
REVERT: A  575 MET cc_start: 0.8091 (tmm) cc_final: 0.7655 (tmm)
REVERT: A  694 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6597 (mp0)
REVERT: B  198 PHE cc_start: 0.7398 (t80) cc_final: 0.6835 (t80)
REVERT: B  227 LYS cc_start: 0.7834 (ptmt) cc_final: 0.7587 (ptpt)
REVERT: B  694 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6884 (mp0)
  outliers start: 17
  outliers final: 17
  residues processed: 123
  average time/residue: 0.2089
  time to fit residues: 38.2098
Evaluate side-chains
  124 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 1.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  486 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 132 optimal weight:    2.9990
   chunk 84 optimal weight:    9.9990
   chunk 135 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0770
   chunk 115 optimal weight:    5.9990
   chunk 113 optimal weight:    9.9990
   chunk 6 optimal weight:    8.9990
   chunk 40 optimal weight:    5.9990
   chunk 125 optimal weight:    0.0070
   chunk 42 optimal weight:    7.9990
   overall best weight:    1.0160

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 504 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 = 0.3966 r_free = 0.3966 target = 0.144375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.117097 restraints weight = 16420.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 2.35
r_work: 0.3466 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10770  Z= 0.135
  Angle     :  0.526  10.192  14654  Z= 0.254
  Chirality :  0.042   0.127   1744
  Planarity :  0.004   0.056   1812
  Dihedral  :  4.334  55.388   1588
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 15.26 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.24), residues: 1352
  helix:  2.01 (0.18), residues: 888
  sheet:  2.19 (0.70), residues: 52
  loop : -0.60 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP A  70 
 HIS   0.001   0.000   HIS B 220 
 PHE   0.014   0.001   PHE A 198 
 TYR   0.011   0.001   TYR B 313 
 ARG   0.010   0.000   ARG A 576 

********************** 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
  136 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 1.255 
Fit side-chains
REVERT: A   70 TRP cc_start: 0.7883 (p-90) cc_final: 0.7653 (p-90)
REVERT: A  227 LYS cc_start: 0.7891 (ptmt) cc_final: 0.7529 (ptpp)
REVERT: A  575 MET cc_start: 0.8044 (tmm) cc_final: 0.7608 (tmm)
REVERT: A  694 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6561 (mp0)
REVERT: B  198 PHE cc_start: 0.7398 (t80) cc_final: 0.6821 (t80)
REVERT: B  227 LYS cc_start: 0.7809 (ptmt) cc_final: 0.7572 (ptpt)
REVERT: B  694 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6907 (mp0)
  outliers start: 20
  outliers final: 16
  residues processed: 131
  average time/residue: 0.2030
  time to fit residues: 39.5197
Evaluate side-chains
  127 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  486 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 131 optimal weight:    6.9990
   chunk 86 optimal weight:   20.0000
   chunk 71 optimal weight:   30.0000
   chunk 110 optimal weight:    9.9990
   chunk 90 optimal weight:    0.5980
   chunk 89 optimal weight:    4.9990
   chunk 80 optimal weight:    8.9990
   chunk 135 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 133 optimal weight:    2.9990
   overall best weight:    4.1188

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 504 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 = 0.3898 r_free = 0.3898 target = 0.139058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.113660 restraints weight = 16579.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 2.04
r_work: 0.3406 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10770  Z= 0.274
  Angle     :  0.570   7.764  14654  Z= 0.284
  Chirality :  0.043   0.133   1744
  Planarity :  0.004   0.057   1812
  Dihedral  :  4.544  57.685   1588
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 15.52 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.24), residues: 1352
  helix:  1.95 (0.18), residues: 884
  sheet:  1.91 (0.70), residues: 52
  loop : -0.75 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP A  70 
 HIS   0.002   0.001   HIS A 640 
 PHE   0.015   0.001   PHE A 198 
 TYR   0.014   0.001   TYR A 545 
 ARG   0.010   0.001   ARG A 576 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5256.95 seconds
wall clock time: 94 minutes 13.96 seconds (5653.96 seconds total)