Starting phenix.real_space_refine
on Wed Feb 12 06:33:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6bgj_7096/02_2025/6bgj_7096_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6bgj_7096/02_2025/6bgj_7096.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6bgj_7096/02_2025/6bgj_7096.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6bgj_7096/02_2025/6bgj_7096.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6bgj_7096/02_2025/6bgj_7096_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6bgj_7096/02_2025/6bgj_7096_neut.cif"
  }
  resolution = 3.8
  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=  -0.000 sd=   1.000
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: 5
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     S      48      5.16       5
     C    4892      2.51       5
     N    1194      2.21       5
     O    1282      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7418
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 490, 3708
          Classifications: {'peptide': 490}
          Incomplete info: {'truncation_to_alanine': 65}
          Link IDs: {'PTRANS': 19, 'TRANS': 470}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 273
          Unresolved non-hydrogen angles: 348
          Unresolved non-hydrogen dihedrals: 234
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 171
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 6.49, per 1000 atoms: 0.87
  Number of scatterers: 7418
  At special positions: 0
  Unit cell: (103.02, 82.62, 99.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      2     19.99
     S      48     16.00
     O    1282      8.00
     N    1194      7.00
     C    4892      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: 1.75
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1868

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      74.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 292 through 303
      removed outlier: 3.606A  pdb=" N   LEU A 300 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 324
    Processing helix  chain 'A' and resid 325 through 362
      removed outlier: 3.691A  pdb=" N   TYR A 331 " --> pdb=" O   LYS A 327 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE A 332 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE A 343 " --> pdb=" O   THR A 339 " (cutoff:3.500A)
      Proline residue:  A 344  - end of helix
      removed outlier: 3.534A  pdb=" N   VAL A 348 " --> pdb=" O   PRO A 344 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   THR A 359 " --> pdb=" O   TYR A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 375
    Processing helix  chain 'A' and resid 390 through 401
      removed outlier: 3.847A  pdb=" N   ARG A 399 " --> pdb=" O   CYS A 395 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ALA A 400 " --> pdb=" O   ALA A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 404
      No H-bonds generated for 'chain 'A' and resid 402 through 404'
    Processing helix  chain 'A' and resid 407 through 442
      removed outlier: 3.670A  pdb=" N   PHE A 412 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   TYR A 436 " --> pdb=" O   MET A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 505
    Processing helix  chain 'A' and resid 508 through 522
      removed outlier: 3.873A  pdb=" N   ALA A 519 " --> pdb=" O   ALA A 515 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   SER A 522 " --> pdb=" O   LEU A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 565
      removed outlier: 3.584A  pdb=" N   VAL A 539 " --> pdb=" O   THR A 535 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE A 547 " --> pdb=" O   LEU A 543 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL A 552 " --> pdb=" O   LEU A 548 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   TYR A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLY A 554 " --> pdb=" O   ASP A 550 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   CYS A 555 " --> pdb=" O   GLU A 551 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   TRP A 559 " --> pdb=" O   CYS A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 589
      removed outlier: 3.521A  pdb=" N   PHE A 578 " --> pdb=" O   GLU A 574 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LEU A 582 " --> pdb=" O   PHE A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 597
    Processing helix  chain 'A' and resid 627 through 642
      removed outlier: 4.265A  pdb=" N   CYS A 631 " --> pdb=" O   LEU A 627 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE A 636 " --> pdb=" O   ILE A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 689
      removed outlier: 3.684A  pdb=" N   PHE A 687 " --> pdb=" O   GLU A 684 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU A 689 " --> pdb=" O   ASP A 686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 694 through 710
      removed outlier: 3.615A  pdb=" N   GLN A 705 " --> pdb=" O   GLU A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 740
      removed outlier: 3.861A  pdb=" N   ASN A 726 " --> pdb=" O   PHE A 722 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ILE A 729 " --> pdb=" O   LEU A 725 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ARG A 732 " --> pdb=" O   ILE A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 753 through 771
      removed outlier: 3.747A  pdb=" N   TYR A 757 " --> pdb=" O   ILE A 753 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ILE A 759 " --> pdb=" O   ILE A 755 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL A 768 " --> pdb=" O   GLY A 764 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ILE A 769 " --> pdb=" O   LYS A 765 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 776
    Processing helix  chain 'A' and resid 781 through 790
      removed outlier: 5.087A  pdb=" N   TYR A 787 " --> pdb=" O   PRO A 783 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   TYR A 789 " --> pdb=" O   LEU A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 802
      No H-bonds generated for 'chain 'A' and resid 800 through 802'
    Processing helix  chain 'A' and resid 803 through 811
      removed outlier: 3.938A  pdb=" N   SER A 807 " --> pdb=" O   HIS A 803 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   SER A 811 " --> pdb=" O   SER A 807 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 825
    Processing helix  chain 'A' and resid 848 through 850
      No H-bonds generated for 'chain 'A' and resid 848 through 850'
    Processing helix  chain 'A' and resid 851 through 882
      removed outlier: 3.738A  pdb=" N   ALA A 855 " --> pdb=" O   LYS A 851 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL A 856 " --> pdb=" O   ASP A 852 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ASN A 869 " --> pdb=" O   ILE A 865 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   MET A 872 " --> pdb=" O   GLN A 868 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   TRP A 880 " --> pdb=" O   ASP A 876 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE A 882 " --> pdb=" O   VAL A 878 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 303
      removed outlier: 3.606A  pdb=" N   LEU B 300 " --> pdb=" O   ASN B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 324
    Processing helix  chain 'B' and resid 325 through 362
      removed outlier: 3.690A  pdb=" N   TYR B 331 " --> pdb=" O   LYS B 327 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   PHE B 332 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE B 343 " --> pdb=" O   THR B 339 " (cutoff:3.500A)
      Proline residue:  B 344  - end of helix
      removed outlier: 3.535A  pdb=" N   VAL B 348 " --> pdb=" O   PRO B 344 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   THR B 359 " --> pdb=" O   TYR B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 375
    Processing helix  chain 'B' and resid 390 through 401
      removed outlier: 3.847A  pdb=" N   ARG B 399 " --> pdb=" O   CYS B 395 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ALA B 400 " --> pdb=" O   ALA B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 404
      No H-bonds generated for 'chain 'B' and resid 402 through 404'
    Processing helix  chain 'B' and resid 407 through 442
      removed outlier: 3.670A  pdb=" N   PHE B 412 " --> pdb=" O   ALA B 408 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   TYR B 436 " --> pdb=" O   MET B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 505
    Processing helix  chain 'B' and resid 508 through 522
      removed outlier: 3.873A  pdb=" N   ALA B 519 " --> pdb=" O   ALA B 515 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   SER B 522 " --> pdb=" O   LEU B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 529 through 565
      removed outlier: 3.584A  pdb=" N   VAL B 539 " --> pdb=" O   THR B 535 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE B 547 " --> pdb=" O   LEU B 543 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL B 552 " --> pdb=" O   LEU B 548 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   TYR B 553 " --> pdb=" O   LEU B 549 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLY B 554 " --> pdb=" O   ASP B 550 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   CYS B 555 " --> pdb=" O   GLU B 551 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   TRP B 559 " --> pdb=" O   CYS B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 568 through 589
      removed outlier: 3.521A  pdb=" N   PHE B 578 " --> pdb=" O   GLU B 574 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LEU B 582 " --> pdb=" O   PHE B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 589 through 597
    Processing helix  chain 'B' and resid 627 through 642
      removed outlier: 4.265A  pdb=" N   CYS B 631 " --> pdb=" O   LEU B 627 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE B 636 " --> pdb=" O   ILE B 632 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 683 through 689
      removed outlier: 3.683A  pdb=" N   PHE B 687 " --> pdb=" O   GLU B 684 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU B 689 " --> pdb=" O   ASP B 686 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 694 through 710
      removed outlier: 3.614A  pdb=" N   GLN B 705 " --> pdb=" O   GLU B 701 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 718 through 740
      removed outlier: 3.861A  pdb=" N   ASN B 726 " --> pdb=" O   PHE B 722 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ILE B 729 " --> pdb=" O   LEU B 725 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ARG B 732 " --> pdb=" O   ILE B 728 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 753 through 771
      removed outlier: 3.748A  pdb=" N   TYR B 757 " --> pdb=" O   ILE B 753 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ILE B 759 " --> pdb=" O   ILE B 755 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL B 768 " --> pdb=" O   GLY B 764 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ILE B 769 " --> pdb=" O   LYS B 765 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 771 through 776
    Processing helix  chain 'B' and resid 781 through 790
      removed outlier: 5.086A  pdb=" N   TYR B 787 " --> pdb=" O   PRO B 783 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   TYR B 789 " --> pdb=" O   LEU B 785 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 800 through 802
      No H-bonds generated for 'chain 'B' and resid 800 through 802'
    Processing helix  chain 'B' and resid 803 through 811
      removed outlier: 3.937A  pdb=" N   SER B 807 " --> pdb=" O   HIS B 803 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   SER B 811 " --> pdb=" O   SER B 807 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 820 through 825
    Processing helix  chain 'B' and resid 848 through 850
      No H-bonds generated for 'chain 'B' and resid 848 through 850'
    Processing helix  chain 'B' and resid 851 through 882
      removed outlier: 3.738A  pdb=" N   ALA B 855 " --> pdb=" O   LYS B 851 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL B 856 " --> pdb=" O   ASP B 852 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ASN B 869 " --> pdb=" O   ILE B 865 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   MET B 872 " --> pdb=" O   GLN B 868 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   TRP B 880 " --> pdb=" O   ASP B 876 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ILE B 882 " --> pdb=" O   VAL B 878 " (cutoff:3.500A)

    453 hydrogen bonds defined for protein.
    1347 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: 1.99

  Time building geometry restraints manager: 2.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2247
        1.34 -     1.46: 1907
        1.46 -     1.58: 3372
        1.58 -     1.70: 0
        1.70 -     1.82: 76
  Bond restraints: 7602
  Sorted by residual:
  bond pdb=" C   ILE A 782 "
       pdb=" N   PRO A 783 "
    ideal  model  delta    sigma   weight residual
    1.334  1.382 -0.048 8.40e-03 1.42e+04 3.28e+01
  bond pdb=" C   ILE B 782 "
       pdb=" N   PRO B 783 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 8.40e-03 1.42e+04 3.15e+01
  bond pdb=" CG1 ILE A 775 "
       pdb=" CD1 ILE A 775 "
    ideal  model  delta    sigma   weight residual
    1.513  1.408  0.105 3.90e-02 6.57e+02 7.30e+00
  bond pdb=" CG1 ILE B 775 "
       pdb=" CD1 ILE B 775 "
    ideal  model  delta    sigma   weight residual
    1.513  1.408  0.105 3.90e-02 6.57e+02 7.22e+00
  bond pdb=" N   SER A 811 "
       pdb=" CA  SER A 811 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.029 1.29e-02 6.01e+03 5.18e+00
  ... (remaining 7597 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 9642
        2.12 -     4.23: 555
        4.23 -     6.35: 125
        6.35 -     8.46: 28
        8.46 -    10.58: 10
  Bond angle restraints: 10360
  Sorted by residual:
  angle pdb=" C   ASN A 809 "
        pdb=" N   VAL A 810 "
        pdb=" CA  VAL A 810 "
      ideal   model   delta    sigma   weight residual
     121.97  130.80   -8.83 1.80e+00 3.09e-01 2.41e+01
  angle pdb=" C   SER B 522 "
        pdb=" N   SER B 523 "
        pdb=" CA  SER B 523 "
      ideal   model   delta    sigma   weight residual
     122.83  128.12   -5.29 1.08e+00 8.57e-01 2.40e+01
  angle pdb=" C   ASN B 809 "
        pdb=" N   VAL B 810 "
        pdb=" CA  VAL B 810 "
      ideal   model   delta    sigma   weight residual
     121.97  130.77   -8.80 1.80e+00 3.09e-01 2.39e+01
  angle pdb=" C   SER A 522 "
        pdb=" N   SER A 523 "
        pdb=" CA  SER A 523 "
      ideal   model   delta    sigma   weight residual
     122.83  128.10   -5.27 1.08e+00 8.57e-01 2.38e+01
  angle pdb=" N   ASP B 752 "
        pdb=" CA  ASP B 752 "
        pdb=" C   ASP B 752 "
      ideal   model   delta    sigma   weight residual
     110.91  116.49   -5.58 1.17e+00 7.31e-01 2.28e+01
  ... (remaining 10355 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.03: 3780
       11.03 -    22.06: 543
       22.06 -    33.10: 59
       33.10 -    44.13: 28
       44.13 -    55.16: 10
  Dihedral angle restraints: 4420
    sinusoidal: 1538
      harmonic: 2882
  Sorted by residual:
  dihedral pdb=" CA  GLN A 793 "
           pdb=" C   GLN A 793 "
           pdb=" N   ASN A 794 "
           pdb=" CA  ASN A 794 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  124.84   55.16     0      5.00e+00 4.00e-02 1.22e+02
  dihedral pdb=" CA  GLN B 793 "
           pdb=" C   GLN B 793 "
           pdb=" N   ASN B 794 "
           pdb=" CA  ASN B 794 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  124.90   55.10     0      5.00e+00 4.00e-02 1.21e+02
  dihedral pdb=" CA  ASN A 809 "
           pdb=" C   ASN A 809 "
           pdb=" N   VAL A 810 "
           pdb=" CA  VAL A 810 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.12   45.88     0      5.00e+00 4.00e-02 8.42e+01
  ... (remaining 4417 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1014
       0.081 -    0.161: 174
       0.161 -    0.241: 14
       0.241 -    0.322: 0
       0.322 -    0.402: 2
  Chirality restraints: 1204
  Sorted by residual:
  chirality pdb=" CB  ILE A 364 "
            pdb=" CA  ILE A 364 "
            pdb=" CG1 ILE A 364 "
            pdb=" CG2 ILE A 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.24    0.40 2.00e-01 2.50e+01 4.04e+00
  chirality pdb=" CB  ILE B 364 "
            pdb=" CA  ILE B 364 "
            pdb=" CG1 ILE B 364 "
            pdb=" CG2 ILE B 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.24    0.40 2.00e-01 2.50e+01 4.03e+00
  chirality pdb=" CB  VAL A 713 "
            pdb=" CA  VAL A 713 "
            pdb=" CG1 VAL A 713 "
            pdb=" CG2 VAL A 713 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 1201 not shown)

  Planarity restraints: 1298
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 379 "   -0.059 5.00e-02 4.00e+02   8.88e-02 1.26e+01
        pdb=" N   PRO A 380 "    0.153 5.00e-02 4.00e+02
        pdb=" CA  PRO A 380 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 380 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 379 "   -0.059 5.00e-02 4.00e+02   8.87e-02 1.26e+01
        pdb=" N   PRO B 380 "    0.153 5.00e-02 4.00e+02
        pdb=" CA  PRO B 380 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO B 380 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 622 "    0.056 5.00e-02 4.00e+02   8.41e-02 1.13e+01
        pdb=" N   PRO B 623 "   -0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO B 623 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO B 623 "    0.047 5.00e-02 4.00e+02
  ... (remaining 1295 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 177
        2.69 -     3.25: 7668
        3.25 -     3.80: 11542
        3.80 -     4.35: 15421
        4.35 -     4.90: 24120
  Nonbonded interactions: 58928
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 383 "
            pdb=" NH2 ARG B 614 "
     model   vdw
     2.142 3.120
  nonbonded pdb=" OD2 ASP A 383 "
            pdb=" NH2 ARG A 614 "
     model   vdw
     2.142 3.120
  nonbonded pdb=" NH2 ARG B 321 "
            pdb=" OE2 GLU B 326 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" NH2 ARG A 321 "
            pdb=" OE2 GLU A 326 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" OD2 ASP A 821 "
            pdb=" N   LYS A 846 "
     model   vdw
     2.225 3.120
  ... (remaining 58923 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.810
  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:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     21.320
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  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:2.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5961
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      :  0.008   0.105   7602  Z= 0.515
  Angle     :  1.211  10.576  10360  Z= 0.673
  Chirality :  0.060   0.402   1204
  Planarity :  0.010   0.089   1298
  Dihedral  : 10.716  55.160   2552
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 13.69 %
    Favored  : 85.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 2.14 %

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: -5.82 (0.19), residues: 964
  helix: -3.34 (0.14), residues: 582
  sheet:  None (None), residues: 0
  loop : -4.63 (0.25), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP B 427 
 HIS   0.011   0.004   HIS A 803 
 PHE   0.044   0.004   PHE A 353 
 TYR   0.036   0.003   TYR A 338 
 ARG   0.006   0.001   ARG A 373 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.829 
Fit side-chains
REVERT: A  319 LEU cc_start: 0.8068 (tp) cc_final: 0.7828 (tp)
REVERT: A  321 ARG cc_start: 0.5258 (tmt-80) cc_final: 0.4605 (ttm170)
REVERT: A  618 MET cc_start: 0.3858 (tpt) cc_final: 0.3413 (mtt)
REVERT: A  633 GLN cc_start: 0.5444 (mt0) cc_final: 0.5038 (mt0)
REVERT: A  702 MET cc_start: 0.7551 (tpp) cc_final: 0.7304 (tpp)
REVERT: B  319 LEU cc_start: 0.7988 (tp) cc_final: 0.7774 (tp)
REVERT: B  574 GLU cc_start: 0.7249 (mm-30) cc_final: 0.7034 (mm-30)
REVERT: B  618 MET cc_start: 0.3842 (tpt) cc_final: 0.3482 (mtm)
REVERT: B  633 GLN cc_start: 0.5766 (mt0) cc_final: 0.5317 (mt0)
REVERT: B  725 LEU cc_start: 0.7238 (mt) cc_final: 0.6899 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.1770
  time to fit residues: 53.4283
Evaluate side-chains
  158 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.4980
   chunk 74 optimal weight:    0.0970
   chunk 41 optimal weight:    0.9990
   chunk 25 optimal weight:    0.1980
   chunk 50 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A 372 GLN
A 645 GLN
** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 803 HIS
A 809 ASN
B 645 GLN
** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 809 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4852 r_free = 0.4852 target = 0.232845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.201838 restraints weight = 10274.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.203581 restraints weight = 7993.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.203827 restraints weight = 6856.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.4566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6101
moved from start:          0.3054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7602  Z= 0.249
  Angle     :  0.888  11.689  10360  Z= 0.461
  Chirality :  0.048   0.193   1204
  Planarity :  0.007   0.058   1298
  Dihedral  :  8.299  46.560   1048
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 11.41 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  9.64 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.07 %

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: -4.25 (0.22), residues: 964
  helix: -1.87 (0.17), residues: 658
  sheet:  None (None), residues: 0
  loop : -4.84 (0.28), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 419 
 HIS   0.009   0.003   HIS B 803 
 PHE   0.025   0.002   PHE B 873 
 TYR   0.023   0.002   TYR B 847 
 ARG   0.005   0.001   ARG A 860 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 170
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
REVERT: A  318 ASP cc_start: 0.6035 (p0) cc_final: 0.5771 (p0)
REVERT: A  351 ILE cc_start: 0.8189 (mt) cc_final: 0.7914 (mm)
REVERT: A  353 PHE cc_start: 0.5966 (OUTLIER) cc_final: 0.5732 (m-80)
REVERT: A  618 MET cc_start: 0.4099 (tpt) cc_final: 0.3755 (mtm)
REVERT: A  702 MET cc_start: 0.7247 (tpp) cc_final: 0.6679 (mmp)
REVERT: A  718 LEU cc_start: 0.8598 (tt) cc_final: 0.7695 (pt)
REVERT: A  755 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6897 (mt)
REVERT: B  318 ASP cc_start: 0.5858 (p0) cc_final: 0.5554 (p0)
REVERT: B  587 ASN cc_start: 0.7578 (t0) cc_final: 0.7339 (t0)
REVERT: B  612 ILE cc_start: -0.1343 (OUTLIER) cc_final: -0.2385 (tp)
REVERT: B  633 GLN cc_start: 0.4773 (mt0) cc_final: 0.4532 (mt0)
REVERT: B  790 MET cc_start: 0.4099 (mmt) cc_final: 0.3895 (mmp)
  outliers start: 15
  outliers final: 3
  residues processed: 172
  average time/residue: 0.1643
  time to fit residues: 39.4414
Evaluate side-chains
  155 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 149
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 PHE
Chi-restraints excluded: chain A residue  755 ILE
Chi-restraints excluded: chain B residue  367 MET
Chi-restraints excluded: chain B residue  369 MET
Chi-restraints excluded: chain B residue  612 ILE
Chi-restraints excluded: chain B residue  728 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 85 optimal weight:    0.0980
   chunk 21 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 18 optimal weight:    9.9990
   chunk 91 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 87 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 645 GLN
** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 803 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4847 r_free = 0.4847 target = 0.231386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.195373 restraints weight = 10407.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.199190 restraints weight = 6864.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.201320 restraints weight = 5268.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.4549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6122
moved from start:          0.3876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7602  Z= 0.226
  Angle     :  0.809  13.351  10360  Z= 0.418
  Chirality :  0.046   0.222   1204
  Planarity :  0.006   0.057   1298
  Dihedral  :  7.618  42.671   1048
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  : 12.97 %
    Favored  : 86.62 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 12.40 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.96 %

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: -3.43 (0.23), residues: 964
  helix: -1.25 (0.17), residues: 668
  sheet:  None (None), residues: 0
  loop : -4.64 (0.29), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 334 
 HIS   0.011   0.003   HIS A 803 
 PHE   0.025   0.002   PHE A 873 
 TYR   0.025   0.002   TYR B 847 
 ARG   0.005   0.001   ARG A 373 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 166
  time to evaluate  : 0.784 
Fit side-chains
REVERT: A  321 ARG cc_start: 0.5102 (tmt-80) cc_final: 0.4150 (ttm170)
REVERT: A  351 ILE cc_start: 0.8342 (mt) cc_final: 0.8036 (mm)
REVERT: A  353 PHE cc_start: 0.6330 (OUTLIER) cc_final: 0.6062 (m-80)
REVERT: A  367 MET cc_start: 0.3447 (ptm) cc_final: 0.3184 (ppp)
REVERT: A  368 GLU cc_start: 0.7398 (pm20) cc_final: 0.6999 (pm20)
REVERT: A  618 MET cc_start: 0.3869 (tpt) cc_final: 0.3589 (mtm)
REVERT: A  633 GLN cc_start: 0.5188 (mt0) cc_final: 0.4658 (mt0)
REVERT: A  702 MET cc_start: 0.7605 (tpp) cc_final: 0.6951 (mmp)
REVERT: A  718 LEU cc_start: 0.8534 (tt) cc_final: 0.7407 (pt)
REVERT: A  755 ILE cc_start: 0.6841 (OUTLIER) cc_final: 0.6626 (mt)
REVERT: A  797 MET cc_start: 0.0948 (mpp) cc_final: 0.0610 (mtt)
REVERT: B  321 ARG cc_start: 0.4901 (tmt-80) cc_final: 0.4245 (ttm170)
REVERT: B  341 MET cc_start: 0.7285 (mtm) cc_final: 0.7050 (mtm)
REVERT: B  353 PHE cc_start: 0.6305 (OUTLIER) cc_final: 0.5958 (m-80)
REVERT: B  411 PHE cc_start: 0.6992 (t80) cc_final: 0.6767 (t80)
REVERT: B  574 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6313 (mm-30)
REVERT: B  790 MET cc_start: 0.3878 (mmt) cc_final: 0.3663 (mmt)
REVERT: B  797 MET cc_start: 0.2094 (mpp) cc_final: 0.1600 (mmt)
REVERT: B  873 PHE cc_start: 0.6721 (t80) cc_final: 0.6487 (t80)
  outliers start: 15
  outliers final: 6
  residues processed: 173
  average time/residue: 0.1663
  time to fit residues: 39.9194
Evaluate side-chains
  145 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 PHE
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  413 SER
Chi-restraints excluded: chain A residue  755 ILE
Chi-restraints excluded: chain B residue  353 PHE
Chi-restraints excluded: chain B residue  367 MET
Chi-restraints excluded: chain B residue  369 MET
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  577 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 94 optimal weight:    0.2980
   chunk 6 optimal weight:    1.9990
   chunk 50 optimal weight:   20.0000
   chunk 12 optimal weight:    0.4980
   chunk 46 optimal weight:    0.5980
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 8 optimal weight:    0.3980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 645 GLN
** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4868 r_free = 0.4868 target = 0.234329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.196230 restraints weight = 10396.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.200352 restraints weight = 6866.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.203105 restraints weight = 5266.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.4566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6098
moved from start:          0.4441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7602  Z= 0.214
  Angle     :  0.775  12.071  10360  Z= 0.400
  Chirality :  0.046   0.200   1204
  Planarity :  0.005   0.052   1298
  Dihedral  :  7.163  42.068   1048
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.34 %
    Favored  : 87.45 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.64 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.75 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.25), residues: 964
  helix: -0.63 (0.19), residues: 676
  sheet:  None (None), residues: 0
  loop : -4.39 (0.31), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 305 
 HIS   0.007   0.002   HIS A 803 
 PHE   0.020   0.002   PHE A 873 
 TYR   0.020   0.001   TYR B 847 
 ARG   0.005   0.000   ARG B 373 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 155
  time to evaluate  : 0.837 
Fit side-chains
REVERT: A  321 ARG cc_start: 0.4981 (tmt-80) cc_final: 0.3948 (ttm170)
REVERT: A  351 ILE cc_start: 0.8277 (mt) cc_final: 0.7986 (mm)
REVERT: A  367 MET cc_start: 0.3514 (ptm) cc_final: 0.2940 (ppp)
REVERT: A  368 GLU cc_start: 0.7549 (pm20) cc_final: 0.7043 (pm20)
REVERT: A  618 MET cc_start: 0.3797 (tpt) cc_final: 0.3595 (mtt)
REVERT: A  633 GLN cc_start: 0.5240 (mt0) cc_final: 0.4690 (mt0)
REVERT: A  642 GLN cc_start: 0.5961 (mm-40) cc_final: 0.5465 (mm-40)
REVERT: A  702 MET cc_start: 0.7447 (tpp) cc_final: 0.7190 (mmp)
REVERT: A  755 ILE cc_start: 0.6673 (OUTLIER) cc_final: 0.6461 (mt)
REVERT: A  797 MET cc_start: 0.0955 (mpp) cc_final: 0.0696 (mtt)
REVERT: B  321 ARG cc_start: 0.5015 (tmt-80) cc_final: 0.4050 (ttm170)
REVERT: B  348 VAL cc_start: 0.7378 (m) cc_final: 0.7156 (t)
REVERT: B  353 PHE cc_start: 0.6374 (OUTLIER) cc_final: 0.6000 (m-80)
REVERT: B  391 MET cc_start: 0.2715 (OUTLIER) cc_final: 0.2139 (mtm)
REVERT: B  411 PHE cc_start: 0.7004 (t80) cc_final: 0.6803 (t80)
REVERT: B  574 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6244 (mm-30)
REVERT: B  633 GLN cc_start: 0.5612 (mt0) cc_final: 0.4897 (mt0)
REVERT: B  790 MET cc_start: 0.3902 (mmt) cc_final: 0.3645 (mmt)
REVERT: B  797 MET cc_start: 0.2235 (mpp) cc_final: 0.1692 (mmt)
REVERT: B  873 PHE cc_start: 0.6585 (t80) cc_final: 0.6346 (t80)
  outliers start: 13
  outliers final: 5
  residues processed: 159
  average time/residue: 0.1747
  time to fit residues: 38.2903
Evaluate side-chains
  148 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 140
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain A residue  755 ILE
Chi-restraints excluded: chain B residue  353 PHE
Chi-restraints excluded: chain B residue  369 MET
Chi-restraints excluded: chain B residue  391 MET
Chi-restraints excluded: chain B residue  552 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   chunk 18 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0070
   chunk 28 optimal weight:    0.9990
   chunk 25 optimal weight:    0.1980
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
A 372 GLN
** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4882 r_free = 0.4882 target = 0.235179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.197140 restraints weight = 10252.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.200988 restraints weight = 6893.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.203220 restraints weight = 5379.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.4568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6082
moved from start:          0.4847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7602  Z= 0.206
  Angle     :  0.761  14.105  10360  Z= 0.387
  Chirality :  0.045   0.202   1204
  Planarity :  0.005   0.049   1298
  Dihedral  :  6.864  41.229   1048
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 11.83 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.09 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.54 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.26), residues: 964
  helix: -0.14 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -4.29 (0.31), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 305 
 HIS   0.005   0.001   HIS A 803 
 PHE   0.017   0.002   PHE A 877 
 TYR   0.019   0.001   TYR A 355 
 ARG   0.004   0.000   ARG B 373 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 154
  time to evaluate  : 0.862 
Fit side-chains
REVERT: A  321 ARG cc_start: 0.5128 (tmt-80) cc_final: 0.3916 (ttm170)
REVERT: A  341 MET cc_start: 0.7110 (mtm) cc_final: 0.6590 (mtm)
REVERT: A  367 MET cc_start: 0.3741 (ptm) cc_final: 0.3233 (ppp)
REVERT: A  368 GLU cc_start: 0.7667 (pm20) cc_final: 0.7172 (pm20)
REVERT: A  391 MET cc_start: 0.3948 (OUTLIER) cc_final: 0.3378 (mpt)
REVERT: A  411 PHE cc_start: 0.6882 (t80) cc_final: 0.6425 (t80)
REVERT: A  633 GLN cc_start: 0.4993 (mt0) cc_final: 0.4482 (mt0)
REVERT: A  642 GLN cc_start: 0.5885 (mm-40) cc_final: 0.5394 (mm-40)
REVERT: A  702 MET cc_start: 0.7463 (tpp) cc_final: 0.6926 (mmp)
REVERT: A  755 ILE cc_start: 0.6541 (OUTLIER) cc_final: 0.6236 (mt)
REVERT: B  321 ARG cc_start: 0.5147 (tmt-80) cc_final: 0.4043 (ttm170)
REVERT: B  348 VAL cc_start: 0.7427 (m) cc_final: 0.7206 (t)
REVERT: B  353 PHE cc_start: 0.6380 (OUTLIER) cc_final: 0.5969 (m-10)
REVERT: B  391 MET cc_start: 0.2631 (OUTLIER) cc_final: 0.1797 (mtm)
REVERT: B  633 GLN cc_start: 0.5429 (mt0) cc_final: 0.4703 (mt0)
REVERT: B  755 ILE cc_start: 0.6575 (mm) cc_final: 0.6353 (mm)
REVERT: B  797 MET cc_start: 0.2237 (mpp) cc_final: 0.1685 (mmt)
  outliers start: 17
  outliers final: 6
  residues processed: 159
  average time/residue: 0.1743
  time to fit residues: 38.3932
Evaluate side-chains
  153 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 143
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  755 ILE
Chi-restraints excluded: chain B residue  353 PHE
Chi-restraints excluded: chain B residue  369 MET
Chi-restraints excluded: chain B residue  391 MET
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  577 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    0.0870
   chunk 55 optimal weight:    0.6980
   chunk 81 optimal weight:    0.5980
   chunk 19 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 89 optimal weight:    0.3980
   chunk 88 optimal weight:    0.6980
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 758 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4893 r_free = 0.4893 target = 0.235742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.200646 restraints weight = 10150.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.202698 restraints weight = 7549.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.203848 restraints weight = 5946.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.4580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6089
moved from start:          0.5079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7602  Z= 0.206
  Angle     :  0.763  11.002  10360  Z= 0.392
  Chirality :  0.046   0.221   1204
  Planarity :  0.005   0.045   1298
  Dihedral  :  6.708  40.958   1048
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 11.93 %
    Favored  : 87.86 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.46 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.64 %

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 (0.27), residues: 964
  helix:  0.07 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -4.37 (0.31), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 305 
 HIS   0.005   0.001   HIS A 803 
 PHE   0.017   0.002   PHE A 873 
 TYR   0.011   0.001   TYR B 338 
 ARG   0.005   0.000   ARG B 373 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 153
  time to evaluate  : 0.843 
Fit side-chains
REVERT: A  321 ARG cc_start: 0.5308 (tmt-80) cc_final: 0.3790 (ttm170)
REVERT: A  348 VAL cc_start: 0.7366 (m) cc_final: 0.7064 (t)
REVERT: A  367 MET cc_start: 0.3820 (ptm) cc_final: 0.3200 (ppp)
REVERT: A  368 GLU cc_start: 0.7659 (pm20) cc_final: 0.7146 (pm20)
REVERT: A  391 MET cc_start: 0.3302 (OUTLIER) cc_final: 0.3079 (mpt)
REVERT: A  411 PHE cc_start: 0.6879 (t80) cc_final: 0.6406 (t80)
REVERT: A  633 GLN cc_start: 0.4962 (mt0) cc_final: 0.4494 (mt0)
REVERT: A  642 GLN cc_start: 0.5718 (mm-40) cc_final: 0.5177 (mm-40)
REVERT: A  702 MET cc_start: 0.7450 (tpp) cc_final: 0.6973 (mmp)
REVERT: A  718 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6750 (mt)
REVERT: B  353 PHE cc_start: 0.6238 (OUTLIER) cc_final: 0.5860 (m-10)
REVERT: B  574 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6636 (tp30)
REVERT: B  633 GLN cc_start: 0.5307 (mt0) cc_final: 0.4584 (mt0)
REVERT: B  645 GLN cc_start: 0.6007 (pp30) cc_final: 0.4467 (tp-100)
REVERT: B  797 MET cc_start: 0.2182 (mpp) cc_final: 0.1633 (mmt)
REVERT: B  873 PHE cc_start: 0.6771 (t80) cc_final: 0.6504 (t80)
  outliers start: 15
  outliers final: 7
  residues processed: 156
  average time/residue: 0.1668
  time to fit residues: 36.7885
Evaluate side-chains
  150 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue  353 PHE
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  577 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 73 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0980
   chunk 90 optimal weight:    0.0970
   chunk 39 optimal weight:    0.7980
   chunk 88 optimal weight:    0.6980
   chunk 50 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9990
   chunk 92 optimal weight:    0.0370
   overall best weight:    0.3056

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

Flipped N/Q/H residues before XYZ refinement:
A 705 GLN
A 802 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4911 r_free = 0.4911 target = 0.237961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.203645 restraints weight = 9947.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.206035 restraints weight = 7497.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.207088 restraints weight = 5844.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.4608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6032
moved from start:          0.5371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7602  Z= 0.199
  Angle     :  0.763  10.759  10360  Z= 0.394
  Chirality :  0.045   0.195   1204
  Planarity :  0.005   0.043   1298
  Dihedral  :  6.636  50.102   1048
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.03 %
    Favored  : 87.76 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.29 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.64 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.27), residues: 964
  helix:  0.06 (0.20), residues: 700
  sheet:  None (None), residues: 0
  loop : -4.47 (0.32), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 305 
 HIS   0.005   0.001   HIS A 803 
 PHE   0.016   0.002   PHE B 873 
 TYR   0.009   0.001   TYR A 338 
 ARG   0.004   0.000   ARG B 373 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 153
  time to evaluate  : 0.829 
Fit side-chains
REVERT: A  321 ARG cc_start: 0.5068 (tmt-80) cc_final: 0.3463 (ttm170)
REVERT: A  367 MET cc_start: 0.3724 (ptm) cc_final: 0.3142 (ppp)
REVERT: A  368 GLU cc_start: 0.7561 (pm20) cc_final: 0.7029 (pm20)
REVERT: A  391 MET cc_start: 0.3999 (OUTLIER) cc_final: 0.2207 (mtp)
REVERT: A  633 GLN cc_start: 0.4939 (mt0) cc_final: 0.4475 (mt0)
REVERT: A  642 GLN cc_start: 0.5542 (mm-40) cc_final: 0.4933 (mm-40)
REVERT: A  702 MET cc_start: 0.7434 (tpp) cc_final: 0.7189 (mmp)
REVERT: A  718 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6703 (mt)
REVERT: B  353 PHE cc_start: 0.6220 (OUTLIER) cc_final: 0.5847 (m-10)
REVERT: B  574 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6075 (mm-30)
REVERT: B  633 GLN cc_start: 0.5216 (mt0) cc_final: 0.4533 (mt0)
REVERT: B  718 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7539 (tp)
REVERT: B  797 MET cc_start: 0.2238 (mpp) cc_final: 0.1680 (mmt)
  outliers start: 12
  outliers final: 6
  residues processed: 156
  average time/residue: 0.1785
  time to fit residues: 38.5134
Evaluate side-chains
  147 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 137
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  353 PHE
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  718 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 81 optimal weight:    0.4980
   chunk 65 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 642 GLN
A 645 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4891 r_free = 0.4891 target = 0.235177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.197571 restraints weight = 10522.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.201478 restraints weight = 7085.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.204078 restraints weight = 5514.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.4582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6079
moved from start:          0.5503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   7602  Z= 0.232
  Angle     :  0.806  10.551  10360  Z= 0.414
  Chirality :  0.047   0.203   1204
  Planarity :  0.005   0.046   1298
  Dihedral  :  6.565  47.437   1048
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.55 %
    Favored  : 87.24 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.94 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.64 %

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: -1.52 (0.27), residues: 964
  helix:  0.27 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop : -4.34 (0.31), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 427 
 HIS   0.004   0.001   HIS B 803 
 PHE   0.014   0.002   PHE A 585 
 TYR   0.016   0.001   TYR A 338 
 ARG   0.003   0.000   ARG B 860 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 145
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A  321 ARG cc_start: 0.5068 (tmt-80) cc_final: 0.3351 (ttm170)
REVERT: A  367 MET cc_start: 0.3680 (ptm) cc_final: 0.3130 (ppp)
REVERT: A  368 GLU cc_start: 0.7504 (pm20) cc_final: 0.7196 (pm20)
REVERT: A  378 MET cc_start: 0.2431 (ptm) cc_final: 0.1680 (ptm)
REVERT: A  391 MET cc_start: 0.3987 (OUTLIER) cc_final: 0.2916 (mtt)
REVERT: A  633 GLN cc_start: 0.5052 (mt0) cc_final: 0.4557 (mt0)
REVERT: A  718 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6546 (mp)
REVERT: B  321 ARG cc_start: 0.4986 (tmt-80) cc_final: 0.3446 (ttm170)
REVERT: B  353 PHE cc_start: 0.6414 (OUTLIER) cc_final: 0.5971 (m-10)
REVERT: B  633 GLN cc_start: 0.5378 (mt0) cc_final: 0.4889 (mt0)
REVERT: B  797 MET cc_start: 0.2286 (mpp) cc_final: 0.1645 (mmt)
  outliers start: 12
  outliers final: 9
  residues processed: 149
  average time/residue: 0.1684
  time to fit residues: 34.8269
Evaluate side-chains
  147 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  642 GLN
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  353 PHE
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  552 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 43 optimal weight:    0.0970
   chunk 56 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 0 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 81 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0570
   overall best weight:    0.5096

-------------------------------------------------------------------------------
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 = 0.4907 r_free = 0.4907 target = 0.236865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.200389 restraints weight = 10484.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.202623 restraints weight = 7595.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.204235 restraints weight = 6119.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.4580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6078
moved from start:          0.5674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7602  Z= 0.218
  Angle     :  0.775  10.472  10360  Z= 0.401
  Chirality :  0.045   0.191   1204
  Planarity :  0.004   0.043   1298
  Dihedral  :  6.487  45.561   1048
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.14 %
    Favored  : 87.66 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 16.67 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.64 %

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: -1.45 (0.27), residues: 964
  helix:  0.30 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop : -4.27 (0.32), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 427 
 HIS   0.004   0.001   HIS A 803 
 PHE   0.015   0.001   PHE A 585 
 TYR   0.013   0.001   TYR A 338 
 ARG   0.004   0.000   ARG B 373 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 0.798 
Fit side-chains
REVERT: A  321 ARG cc_start: 0.5331 (tmt-80) cc_final: 0.3178 (ttm170)
REVERT: A  367 MET cc_start: 0.3847 (ptm) cc_final: 0.3252 (ppp)
REVERT: A  368 GLU cc_start: 0.7524 (pm20) cc_final: 0.7245 (pm20)
REVERT: A  378 MET cc_start: 0.2250 (ptm) cc_final: 0.1883 (ptm)
REVERT: A  391 MET cc_start: 0.3910 (OUTLIER) cc_final: 0.3284 (mpt)
REVERT: A  633 GLN cc_start: 0.5083 (mt0) cc_final: 0.4583 (mt0)
REVERT: A  718 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6620 (mt)
REVERT: B  341 MET cc_start: 0.6711 (mtm) cc_final: 0.6389 (mtm)
REVERT: B  353 PHE cc_start: 0.6313 (OUTLIER) cc_final: 0.5926 (m-10)
REVERT: B  391 MET cc_start: 0.4644 (mpp) cc_final: 0.2399 (ttt)
REVERT: B  633 GLN cc_start: 0.5288 (mt0) cc_final: 0.4520 (mt0)
REVERT: B  645 GLN cc_start: 0.5725 (pp30) cc_final: 0.3964 (tp-100)
REVERT: B  718 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7576 (tp)
REVERT: B  797 MET cc_start: 0.2192 (mpp) cc_final: 0.1646 (mmt)
  outliers start: 13
  outliers final: 5
  residues processed: 145
  average time/residue: 0.1794
  time to fit residues: 36.5242
Evaluate side-chains
  137 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain B residue  353 PHE
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  718 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 90 optimal weight:    0.0270
   chunk 4 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0770
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
A 820 ASN
** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.236862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.198207 restraints weight = 10461.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.202234 restraints weight = 7095.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.204429 restraints weight = 5506.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.4591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6064
moved from start:          0.5825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7602  Z= 0.221
  Angle     :  0.806  14.436  10360  Z= 0.413
  Chirality :  0.046   0.194   1204
  Planarity :  0.004   0.043   1298
  Dihedral  :  6.427  43.944   1048
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.14 %
    Favored  : 87.66 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 17.77 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.64 %

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: -1.38 (0.27), residues: 964
  helix:  0.38 (0.20), residues: 682
  sheet:  None (None), residues: 0
  loop : -4.30 (0.31), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 427 
 HIS   0.004   0.001   HIS B 803 
 PHE   0.016   0.001   PHE A 585 
 TYR   0.013   0.001   TYR A 338 
 ARG   0.005   0.000   ARG B 321 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 138
  time to evaluate  : 0.839 
Fit side-chains
REVERT: A  321 ARG cc_start: 0.5243 (tmt-80) cc_final: 0.3153 (ttm170)
REVERT: A  367 MET cc_start: 0.3760 (ptm) cc_final: 0.3063 (ppp)
REVERT: A  368 GLU cc_start: 0.7362 (pm20) cc_final: 0.7131 (pm20)
REVERT: A  378 MET cc_start: 0.2408 (ptm) cc_final: 0.2052 (ptm)
REVERT: A  391 MET cc_start: 0.3977 (OUTLIER) cc_final: 0.3392 (mpt)
REVERT: A  633 GLN cc_start: 0.5131 (mt0) cc_final: 0.4583 (mt0)
REVERT: A  718 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6560 (mt)
REVERT: B  318 ASP cc_start: 0.6320 (p0) cc_final: 0.6009 (p0)
REVERT: B  321 ARG cc_start: 0.5168 (tmt-80) cc_final: 0.3256 (ttm170)
REVERT: B  341 MET cc_start: 0.6866 (mtm) cc_final: 0.6488 (mtm)
REVERT: B  353 PHE cc_start: 0.6338 (OUTLIER) cc_final: 0.5902 (m-10)
REVERT: B  391 MET cc_start: 0.4370 (mpp) cc_final: 0.2375 (ttt)
REVERT: B  574 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6681 (mm-30)
REVERT: B  633 GLN cc_start: 0.5162 (mt0) cc_final: 0.4421 (mt0)
REVERT: B  645 GLN cc_start: 0.5723 (pp30) cc_final: 0.3936 (tp-100)
REVERT: B  718 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7535 (tp)
REVERT: B  797 MET cc_start: 0.2055 (mpp) cc_final: 0.1392 (mmt)
  outliers start: 9
  outliers final: 5
  residues processed: 140
  average time/residue: 0.1602
  time to fit residues: 31.7750
Evaluate side-chains
  141 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain B residue  353 PHE
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  718 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 88 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 64 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0770
   chunk 17 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6138

-------------------------------------------------------------------------------
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 = 0.4927 r_free = 0.4927 target = 0.238752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.203552 restraints weight = 9985.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.207325 restraints weight = 6554.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.209930 restraints weight = 5035.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.4628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6004
moved from start:          0.5910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7602  Z= 0.221
  Angle     :  0.796  10.380  10360  Z= 0.411
  Chirality :  0.045   0.192   1204
  Planarity :  0.004   0.041   1298
  Dihedral  :  6.456  51.257   1048
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.03 %
    Favored  : 87.76 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 17.91 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.64 %

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: -1.35 (0.27), residues: 964
  helix:  0.41 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop : -4.33 (0.31), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 427 
 HIS   0.005   0.001   HIS A 803 
 PHE   0.015   0.002   PHE A 585 
 TYR   0.013   0.001   TYR A 338 
 ARG   0.003   0.000   ARG B 373 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2625.89 seconds
wall clock time: 47 minutes 49.57 seconds (2869.57 seconds total)