Starting phenix.real_space_refine
on Mon Nov 17 18:12:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6bgj_7096/11_2025/6bgj_7096_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6bgj_7096/11_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_7096/11_2025/6bgj_7096.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6bgj_7096/11_2025/6bgj_7096.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6bgj_7096/11_2025/6bgj_7096_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6bgj_7096/11_2025/6bgj_7096_neut.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'GLU:plan': 9, 'ASN:plan1': 4, 'HIS:plan': 1, 'ARG:plan': 7, 'GLN:plan1': 2, 'TYR:plan': 3, 'TRP:plan': 3, 'PHE:plan': 2, 'ASP:plan': 5}
          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: 2.76, per 1000 atoms: 0.37
  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: 0.61
  Conformation dependent library (CDL) restraints added in 437.3 milliseconds
  

  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: 0.23
  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: 1.19

  Time building geometry restraints manager: 0.84 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.400
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.080
-------------------------------------------------------------------------------
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= 0.364
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.006   0.001   ARG A 373 
 TYR   0.036   0.003   TYR A 338 
 PHE   0.044   0.004   PHE A 353 
 TRP   0.026   0.003   TRP B 427 
 HIS   0.011   0.004   HIS A 803 

Details of bonding type rmsd
  covalent geometry    : bond        0.00797 ( 7602)
  covalent geometry    : angle       1.21058 (10360)
  hydrogen bonds       : bond        0.32594 (  453)
  hydrogen bonds       : angle      10.35274 ( 1347)

*********************** 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  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 LEU cc_start: 0.8068 (tp) cc_final: 0.7844 (tp)
REVERT: A  321 ARG cc_start: 0.5258 (tmt-80) cc_final: 0.4600 (ttm170)
REVERT: A  618 MET cc_start: 0.3858 (tpt) cc_final: 0.3422 (mtt)
REVERT: A  633 GLN cc_start: 0.5444 (mt0) cc_final: 0.5050 (mt0)
REVERT: A  702 MET cc_start: 0.7551 (tpp) cc_final: 0.7320 (tpp)
REVERT: B  319 LEU cc_start: 0.7988 (tp) cc_final: 0.7782 (tp)
REVERT: B  574 GLU cc_start: 0.7249 (mm-30) cc_final: 0.7037 (mm-30)
REVERT: B  618 MET cc_start: 0.3842 (tpt) cc_final: 0.3481 (mtm)
REVERT: B  633 GLN cc_start: 0.5766 (mt0) cc_final: 0.5330 (mt0)
REVERT: B  718 LEU cc_start: 0.8245 (tt) cc_final: 0.7805 (pt)
REVERT: B  725 LEU cc_start: 0.7238 (mt) cc_final: 0.6886 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0804
  time to fit residues: 24.4588
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  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    0.4980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.1980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   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 372 GLN
A 645 GLN
** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 803 HIS
A 809 ASN
B 645 GLN
** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4844 r_free = 0.4844 target = 0.232103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.197057 restraints weight = 10433.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.200676 restraints weight = 7078.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.203160 restraints weight = 5517.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.204732 restraints weight = 4687.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.205176 restraints weight = 4230.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.4585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6058
moved from start:          0.3010

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= 0.192
  Angle     :  0.879  11.580  10360  Z= 0.458
  Chirality :  0.048   0.176   1204
  Planarity :  0.007   0.060   1298
  Dihedral  :  8.313  47.398   1048
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  : 11.62 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  :  8.95 %
    Favored  : 89.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.25 (0.22), residues: 964
  helix: -1.87 (0.17), residues: 658
  sheet:  None (None), residues: 0
  loop : -4.83 (0.28), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 860 
 TYR   0.021   0.002   TYR A 510 
 PHE   0.027   0.002   PHE B 873 
 TRP   0.014   0.002   TRP A 419 
 HIS   0.007   0.002   HIS B 803 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 7602)
  covalent geometry    : angle       0.87870 (10360)
  hydrogen bonds       : bond        0.06643 (  453)
  hydrogen bonds       : angle       5.71258 ( 1347)

*********************** 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
  186 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 172
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  318 ASP cc_start: 0.6164 (p0) cc_final: 0.5923 (p0)
REVERT: A  351 ILE cc_start: 0.8300 (mt) cc_final: 0.7986 (mm)
REVERT: A  618 MET cc_start: 0.3938 (tpt) cc_final: 0.3595 (mtm)
REVERT: A  633 GLN cc_start: 0.4597 (mt0) cc_final: 0.4346 (mt0)
REVERT: A  702 MET cc_start: 0.7403 (tpp) cc_final: 0.6858 (mmp)
REVERT: B  318 ASP cc_start: 0.6034 (p0) cc_final: 0.5709 (p0)
REVERT: B  633 GLN cc_start: 0.4904 (mt0) cc_final: 0.4609 (mt0)
REVERT: B  790 MET cc_start: 0.4260 (mmt) cc_final: 0.4013 (mmp)
  outliers start: 14
  outliers final: 3
  residues processed: 174
  average time/residue: 0.0766
  time to fit residues: 18.9371
Evaluate side-chains
  153 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 150
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 MET
Chi-restraints excluded: chain B residue  369 MET
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 77 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0980
   chunk 87 optimal weight:    0.9980
   chunk 14 optimal weight:    9.9990
   chunk 64 optimal weight:    0.3980
   chunk 51 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 6 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 ** 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 = 0.4852 r_free = 0.4852 target = 0.231833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.199646 restraints weight = 10273.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.202209 restraints weight = 8013.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.204028 restraints weight = 6219.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.204710 restraints weight = 5704.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.204833 restraints weight = 4922.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.4580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6087
moved from start:          0.3811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7602  Z= 0.170
  Angle     :  0.814  14.232  10360  Z= 0.420
  Chirality :  0.046   0.208   1204
  Planarity :  0.006   0.055   1298
  Dihedral  :  7.698  42.335   1048
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  : 12.14 %
    Favored  : 87.45 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 11.43 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.96 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.54 (0.23), residues: 964
  helix: -1.37 (0.17), residues: 682
  sheet:  None (None), residues: 0
  loop : -4.69 (0.29), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 373 
 TYR   0.029   0.002   TYR B 847 
 PHE   0.026   0.002   PHE A 873 
 TRP   0.009   0.001   TRP B 334 
 HIS   0.007   0.003   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 7602)
  covalent geometry    : angle       0.81353 (10360)
  hydrogen bonds       : bond        0.05717 (  453)
  hydrogen bonds       : angle       5.22467 ( 1347)

*********************** 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
  170 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 158
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A  318 ASP cc_start: 0.6027 (p0) cc_final: 0.5816 (p0)
REVERT: A  321 ARG cc_start: 0.5003 (tmt-80) cc_final: 0.4188 (ttm170)
REVERT: A  351 ILE cc_start: 0.8385 (mt) cc_final: 0.8075 (mm)
REVERT: A  368 GLU cc_start: 0.7308 (pm20) cc_final: 0.6947 (pm20)
REVERT: A  378 MET cc_start: 0.2981 (mtt) cc_final: 0.2587 (mtm)
REVERT: A  391 MET cc_start: 0.3237 (OUTLIER) cc_final: 0.2649 (mtt)
REVERT: A  618 MET cc_start: 0.3986 (tpt) cc_final: 0.3728 (mtm)
REVERT: A  633 GLN cc_start: 0.4738 (mt0) cc_final: 0.4430 (mt0)
REVERT: A  702 MET cc_start: 0.7471 (tpp) cc_final: 0.7207 (mmp)
REVERT: A  797 MET cc_start: 0.1046 (mpp) cc_final: 0.0646 (mtt)
REVERT: B  321 ARG cc_start: 0.4779 (tmt-80) cc_final: 0.4205 (ttm170)
REVERT: B  353 PHE cc_start: 0.6072 (OUTLIER) cc_final: 0.5776 (m-80)
REVERT: B  411 PHE cc_start: 0.6998 (t80) cc_final: 0.6736 (t80)
REVERT: B  633 GLN cc_start: 0.5171 (mt0) cc_final: 0.4945 (mt0)
REVERT: B  790 MET cc_start: 0.3868 (mmt) cc_final: 0.3667 (mmt)
REVERT: B  797 MET cc_start: 0.2095 (mpp) cc_final: 0.1582 (mmt)
REVERT: B  873 PHE cc_start: 0.6840 (t80) cc_final: 0.6566 (t80)
  outliers start: 12
  outliers final: 6
  residues processed: 163
  average time/residue: 0.0806
  time to fit residues: 18.2782
Evaluate side-chains
  142 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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  413 SER
Chi-restraints excluded: chain A residue  577 THR
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 28 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 94 optimal weight:    0.1980
   chunk 41 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 9 optimal weight:    9.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 645 GLN
** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 803 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4864 r_free = 0.4864 target = 0.233510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.199498 restraints weight = 10502.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.201906 restraints weight = 8730.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.202847 restraints weight = 6698.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.203049 restraints weight = 6130.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.203627 restraints weight = 5875.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.4572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6107
moved from start:          0.4322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7602  Z= 0.160
  Angle     :  0.770  12.479  10360  Z= 0.398
  Chirality :  0.045   0.194   1204
  Planarity :  0.005   0.049   1298
  Dihedral  :  7.214  42.302   1048
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.66 %
    Favored  : 87.14 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.36 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.64 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.84 (0.25), residues: 964
  helix: -0.78 (0.18), residues: 676
  sheet:  None (None), residues: 0
  loop : -4.55 (0.30), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 373 
 TYR   0.022   0.002   TYR B 847 
 PHE   0.021   0.002   PHE A 873 
 TRP   0.008   0.001   TRP B 305 
 HIS   0.007   0.002   HIS A 803 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 7602)
  covalent geometry    : angle       0.77018 (10360)
  hydrogen bonds       : bond        0.05110 (  453)
  hydrogen bonds       : angle       4.97901 ( 1347)

*********************** 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
  164 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  321 ARG cc_start: 0.4984 (tmt-80) cc_final: 0.3989 (ttm170)
REVERT: A  351 ILE cc_start: 0.8286 (mt) cc_final: 0.8041 (mm)
REVERT: A  378 MET cc_start: 0.3106 (mtt) cc_final: 0.2832 (mtm)
REVERT: A  642 GLN cc_start: 0.6018 (mm-40) cc_final: 0.5576 (mm-40)
REVERT: A  797 MET cc_start: 0.1044 (mpp) cc_final: 0.0516 (mtt)
REVERT: B  321 ARG cc_start: 0.4905 (tmt-80) cc_final: 0.4016 (ttm170)
REVERT: B  353 PHE cc_start: 0.6247 (OUTLIER) cc_final: 0.5916 (m-80)
REVERT: B  411 PHE cc_start: 0.6974 (t80) cc_final: 0.6756 (t80)
REVERT: B  574 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6449 (mm-30)
REVERT: B  633 GLN cc_start: 0.5191 (mt0) cc_final: 0.4991 (mt0)
REVERT: B  642 GLN cc_start: 0.6135 (mm-40) cc_final: 0.5922 (mm110)
REVERT: B  790 MET cc_start: 0.3866 (mmt) cc_final: 0.3640 (mmt)
REVERT: B  797 MET cc_start: 0.2225 (mpp) cc_final: 0.1701 (mmt)
REVERT: B  873 PHE cc_start: 0.6705 (t80) cc_final: 0.6424 (t80)
  outliers start: 12
  outliers final: 6
  residues processed: 156
  average time/residue: 0.0795
  time to fit residues: 17.3137
Evaluate side-chains
  145 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 138
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain B residue  322 LYS
Chi-restraints excluded: chain B residue  353 PHE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0060
   chunk 56 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 67 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:   10.0000
   chunk 81 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.9000

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

Flipped N/Q/H residues before XYZ refinement:
** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4851 r_free = 0.4851 target = 0.231583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.194441 restraints weight = 10357.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.198197 restraints weight = 7052.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.200796 restraints weight = 5530.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.202117 restraints weight = 4735.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.203004 restraints weight = 4326.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.4572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6112
moved from start:          0.4718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090   7602  Z= 0.170
  Angle     :  0.783  12.580  10360  Z= 0.403
  Chirality :  0.046   0.206   1204
  Planarity :  0.005   0.041   1298
  Dihedral  :  7.006  41.299   1048
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.24 %
    Favored  : 87.55 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 13.22 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.54 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.32 (0.26), residues: 964
  helix: -0.42 (0.19), residues: 698
  sheet:  None (None), residues: 0
  loop : -4.58 (0.31), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 373 
 TYR   0.018   0.002   TYR A 338 
 PHE   0.018   0.002   PHE A 877 
 TRP   0.010   0.001   TRP A 305 
 HIS   0.005   0.001   HIS A 803 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 7602)
  covalent geometry    : angle       0.78282 (10360)
  hydrogen bonds       : bond        0.04896 (  453)
  hydrogen bonds       : angle       4.87015 ( 1347)

*********************** 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
  166 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 148
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A  321 ARG cc_start: 0.5075 (tmt-80) cc_final: 0.3879 (ttm170)
REVERT: A  351 ILE cc_start: 0.8395 (mt) cc_final: 0.8125 (mm)
REVERT: A  633 GLN cc_start: 0.5176 (mt0) cc_final: 0.4532 (mt0)
REVERT: B  321 ARG cc_start: 0.4963 (tmt-80) cc_final: 0.3931 (ttm170)
REVERT: B  353 PHE cc_start: 0.6436 (OUTLIER) cc_final: 0.6014 (m-10)
REVERT: B  368 GLU cc_start: 0.7375 (pm20) cc_final: 0.7167 (pm20)
REVERT: B  574 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6700 (mm-30)
REVERT: B  633 GLN cc_start: 0.5198 (mt0) cc_final: 0.4962 (mt0)
REVERT: B  797 MET cc_start: 0.2215 (mpp) cc_final: 0.1633 (mmt)
REVERT: B  873 PHE cc_start: 0.6780 (t80) cc_final: 0.6572 (t80)
  outliers start: 18
  outliers final: 9
  residues processed: 156
  average time/residue: 0.0764
  time to fit residues: 16.7234
Evaluate side-chains
  143 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 133
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  413 SER
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 B residue  353 PHE
Chi-restraints excluded: chain B residue  369 MET
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain B residue  711 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 96 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0670
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4866 r_free = 0.4866 target = 0.232977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.195178 restraints weight = 10304.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.198865 restraints weight = 7053.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.200993 restraints weight = 5551.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.202979 restraints weight = 4830.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.203332 restraints weight = 4363.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.4576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6100
moved from start:          0.4979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   7602  Z= 0.162
  Angle     :  0.794  11.084  10360  Z= 0.405
  Chirality :  0.046   0.207   1204
  Planarity :  0.005   0.041   1298
  Dihedral  :  6.815  40.859   1048
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.55 %
    Favored  : 87.24 %
  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 : 0.54 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.99 (0.27), residues: 964
  helix: -0.16 (0.19), residues: 704
  sheet:  None (None), residues: 0
  loop : -4.58 (0.31), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 373 
 TYR   0.014   0.001   TYR A 338 
 PHE   0.015   0.002   PHE A 873 
 TRP   0.008   0.001   TRP B 305 
 HIS   0.004   0.001   HIS A 803 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7602)
  covalent geometry    : angle       0.79444 (10360)
  hydrogen bonds       : bond        0.04695 (  453)
  hydrogen bonds       : angle       4.79508 ( 1347)

*********************** 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
  160 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 ARG cc_start: 0.5170 (tmt-80) cc_final: 0.3489 (ttm170)
REVERT: A  351 ILE cc_start: 0.8320 (mt) cc_final: 0.8108 (mm)
REVERT: A  353 PHE cc_start: 0.6425 (OUTLIER) cc_final: 0.5864 (m-80)
REVERT: A  411 PHE cc_start: 0.6937 (t80) cc_final: 0.6455 (t80)
REVERT: A  633 GLN cc_start: 0.5062 (mt0) cc_final: 0.4436 (mt0)
REVERT: A  642 GLN cc_start: 0.6376 (OUTLIER) cc_final: 0.6165 (mm110)
REVERT: B  321 ARG cc_start: 0.4923 (tmt-80) cc_final: 0.3495 (ttm-80)
REVERT: B  353 PHE cc_start: 0.6468 (OUTLIER) cc_final: 0.5965 (m-10)
REVERT: B  574 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6174 (mm-30)
REVERT: B  633 GLN cc_start: 0.5181 (mt0) cc_final: 0.4943 (mt0)
REVERT: B  702 MET cc_start: 0.7336 (mmp) cc_final: 0.7092 (mmp)
REVERT: B  755 ILE cc_start: 0.6662 (mm) cc_final: 0.6122 (mt)
REVERT: B  797 MET cc_start: 0.2320 (mpp) cc_final: 0.1742 (mmt)
  outliers start: 15
  outliers final: 8
  residues processed: 149
  average time/residue: 0.0748
  time to fit residues: 15.6250
Evaluate side-chains
  145 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
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  543 LEU
Chi-restraints excluded: chain A residue  642 GLN
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue  340 GLN
Chi-restraints excluded: chain B residue  353 PHE
Chi-restraints excluded: chain B residue  369 MET
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain B residue  711 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0040
   chunk 90 optimal weight:    0.7980
   chunk 81 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 72 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.1396

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 645 GLN
** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4847 r_free = 0.4847 target = 0.230561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.193795 restraints weight = 10260.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.197614 restraints weight = 6868.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.199718 restraints weight = 5346.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.201568 restraints weight = 4628.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.201928 restraints weight = 4190.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.4564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6118
moved from start:          0.5097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7602  Z= 0.177
  Angle     :  0.809  10.810  10360  Z= 0.413
  Chirality :  0.046   0.215   1204
  Planarity :  0.005   0.045   1298
  Dihedral  :  6.859  49.269   1048
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.34 %
    Favored  : 87.45 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 14.05 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.64 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.91 (0.27), residues: 964
  helix: -0.04 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -4.60 (0.30), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 373 
 TYR   0.019   0.002   TYR A 338 
 PHE   0.027   0.002   PHE B 873 
 TRP   0.009   0.001   TRP A 427 
 HIS   0.005   0.001   HIS B 803 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 7602)
  covalent geometry    : angle       0.80872 (10360)
  hydrogen bonds       : bond        0.04760 (  453)
  hydrogen bonds       : angle       4.82569 ( 1347)

*********************** 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
  164 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A  319 LEU cc_start: 0.7426 (tp) cc_final: 0.7120 (tp)
REVERT: A  321 ARG cc_start: 0.5245 (tmt-80) cc_final: 0.3299 (ttm170)
REVERT: A  351 ILE cc_start: 0.8350 (mt) cc_final: 0.8125 (mm)
REVERT: A  353 PHE cc_start: 0.6506 (OUTLIER) cc_final: 0.5889 (m-80)
REVERT: A  411 PHE cc_start: 0.6955 (t80) cc_final: 0.6474 (t80)
REVERT: A  633 GLN cc_start: 0.5113 (mt0) cc_final: 0.4401 (mt0)
REVERT: A  642 GLN cc_start: 0.6307 (OUTLIER) cc_final: 0.5827 (mm110)
REVERT: B  321 ARG cc_start: 0.5237 (tmt-80) cc_final: 0.3530 (ttm-80)
REVERT: B  353 PHE cc_start: 0.6464 (OUTLIER) cc_final: 0.5971 (m-10)
REVERT: B  574 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6553 (mm-30)
REVERT: B  633 GLN cc_start: 0.5172 (mt0) cc_final: 0.4855 (mt0)
REVERT: B  797 MET cc_start: 0.2218 (mpp) cc_final: 0.1598 (mmt)
REVERT: B  873 PHE cc_start: 0.6735 (t80) cc_final: 0.6504 (t80)
  outliers start: 20
  outliers final: 14
  residues processed: 151
  average time/residue: 0.0725
  time to fit residues: 15.4076
Evaluate side-chains
  153 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 GLN
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  543 LEU
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain A residue  642 GLN
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue  303 GLU
Chi-restraints excluded: chain B residue  340 GLN
Chi-restraints excluded: chain B residue  353 PHE
Chi-restraints excluded: chain B residue  369 MET
Chi-restraints excluded: chain B residue  378 MET
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain B residue  711 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 95 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 92 optimal weight:    0.6980
   chunk 96 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4863 r_free = 0.4863 target = 0.231772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.195199 restraints weight = 10442.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.198892 restraints weight = 7031.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.201373 restraints weight = 5507.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4577 r_free = 0.4577 target = 0.202714 restraints weight = 4727.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.203222 restraints weight = 4321.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.4582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6095
moved from start:          0.5318

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= 0.159
  Angle     :  0.789  10.751  10360  Z= 0.404
  Chirality :  0.046   0.201   1204
  Planarity :  0.005   0.047   1298
  Dihedral  :  6.823  45.543   1048
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.66 %
    Favored  : 87.14 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 15.01 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.64 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.83 (0.27), residues: 964
  helix:  0.03 (0.20), residues: 700
  sheet:  None (None), residues: 0
  loop : -4.69 (0.29), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 373 
 TYR   0.015   0.001   TYR A 338 
 PHE   0.026   0.002   PHE B 873 
 TRP   0.008   0.001   TRP B 305 
 HIS   0.004   0.001   HIS B 803 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 7602)
  covalent geometry    : angle       0.78889 (10360)
  hydrogen bonds       : bond        0.04484 (  453)
  hydrogen bonds       : angle       4.75389 ( 1347)

*********************** 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
  159 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: A  321 ARG cc_start: 0.5276 (tmt-80) cc_final: 0.3198 (ttm170)
REVERT: A  341 MET cc_start: 0.6902 (mtm) cc_final: 0.6606 (mtm)
REVERT: A  351 ILE cc_start: 0.8359 (mt) cc_final: 0.8121 (mm)
REVERT: A  353 PHE cc_start: 0.6541 (OUTLIER) cc_final: 0.5917 (m-80)
REVERT: A  378 MET cc_start: 0.3185 (ptp) cc_final: 0.2207 (ptp)
REVERT: A  391 MET cc_start: 0.4379 (mpp) cc_final: 0.2468 (ttt)
REVERT: A  411 PHE cc_start: 0.6933 (t80) cc_final: 0.6453 (t80)
REVERT: A  633 GLN cc_start: 0.5070 (mt0) cc_final: 0.4378 (mt0)
REVERT: A  638 MET cc_start: 0.6205 (OUTLIER) cc_final: 0.5719 (mmm)
REVERT: B  321 ARG cc_start: 0.5345 (tmt-80) cc_final: 0.3458 (ttm170)
REVERT: B  341 MET cc_start: 0.6915 (mtm) cc_final: 0.6586 (mtm)
REVERT: B  353 PHE cc_start: 0.6399 (OUTLIER) cc_final: 0.5906 (m-10)
REVERT: B  391 MET cc_start: 0.4331 (mmt) cc_final: 0.2788 (ttt)
REVERT: B  574 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6674 (mm-30)
REVERT: B  633 GLN cc_start: 0.5189 (mt0) cc_final: 0.4867 (mt0)
REVERT: B  797 MET cc_start: 0.2199 (mpp) cc_final: 0.1632 (mmt)
  outliers start: 19
  outliers final: 13
  residues processed: 146
  average time/residue: 0.0753
  time to fit residues: 15.6377
Evaluate side-chains
  147 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 GLN
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  543 LEU
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  638 MET
Chi-restraints excluded: chain A residue  642 GLN
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue  340 GLN
Chi-restraints excluded: chain B residue  353 PHE
Chi-restraints excluded: chain B residue  369 MET
Chi-restraints excluded: chain B residue  378 MET
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain B residue  711 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 94 optimal weight:    0.0870
   chunk 21 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 93 optimal weight:    2.9990
   chunk 71 optimal weight:    7.9990
   chunk 49 optimal weight:    8.9990
   chunk 20 optimal weight:    0.7980
   chunk 96 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.9162

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

Flipped N/Q/H residues before XYZ refinement:
** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4856 r_free = 0.4856 target = 0.230613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.195013 restraints weight = 10278.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.197750 restraints weight = 7934.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.198895 restraints weight = 6036.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.199550 restraints weight = 5392.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.199890 restraints weight = 5238.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.4545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6144
moved from start:          0.5459

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= 0.167
  Angle     :  0.811  11.896  10360  Z= 0.413
  Chirality :  0.046   0.191   1204
  Planarity :  0.005   0.048   1298
  Dihedral  :  6.778  44.283   1048
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.86 %
    Favored  : 86.93 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 15.29 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.64 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.75 (0.27), residues: 964
  helix:  0.07 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -4.67 (0.30), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 373 
 TYR   0.016   0.001   TYR A 338 
 PHE   0.024   0.002   PHE B 873 
 TRP   0.008   0.001   TRP A 427 
 HIS   0.005   0.001   HIS B 803 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 7602)
  covalent geometry    : angle       0.81117 (10360)
  hydrogen bonds       : bond        0.04551 (  453)
  hydrogen bonds       : angle       4.76100 ( 1347)

*********************** 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
  155 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: A  321 ARG cc_start: 0.5445 (tmt-80) cc_final: 0.3106 (ttm170)
REVERT: A  351 ILE cc_start: 0.8359 (mt) cc_final: 0.8118 (mm)
REVERT: A  353 PHE cc_start: 0.6533 (OUTLIER) cc_final: 0.5919 (m-80)
REVERT: A  411 PHE cc_start: 0.6927 (t80) cc_final: 0.6424 (t80)
REVERT: A  633 GLN cc_start: 0.5130 (mt0) cc_final: 0.4412 (mt0)
REVERT: A  638 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5987 (mmm)
REVERT: A  642 GLN cc_start: 0.6188 (OUTLIER) cc_final: 0.5322 (mm110)
REVERT: B  321 ARG cc_start: 0.5336 (tmt-80) cc_final: 0.3238 (ttm170)
REVERT: B  353 PHE cc_start: 0.6370 (OUTLIER) cc_final: 0.5953 (m-80)
REVERT: B  391 MET cc_start: 0.4231 (mmt) cc_final: 0.2724 (ttt)
REVERT: B  574 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6627 (mm-30)
REVERT: B  633 GLN cc_start: 0.5247 (mt0) cc_final: 0.4939 (mt0)
REVERT: B  797 MET cc_start: 0.2196 (mpp) cc_final: 0.1638 (mmt)
  outliers start: 21
  outliers final: 14
  residues processed: 141
  average time/residue: 0.0762
  time to fit residues: 15.1850
Evaluate side-chains
  147 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 GLN
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  543 LEU
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  638 MET
Chi-restraints excluded: chain A residue  642 GLN
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain B residue  340 GLN
Chi-restraints excluded: chain B residue  353 PHE
Chi-restraints excluded: chain B residue  369 MET
Chi-restraints excluded: chain B residue  378 MET
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  785 LEU
Chi-restraints excluded: chain B residue  847 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 90 optimal weight:    0.0270
   chunk 31 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0980
   chunk 13 optimal weight:    0.9990
   chunk 9 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   chunk 5 optimal weight:    0.0030
   overall best weight:    0.2848

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

Flipped N/Q/H residues before XYZ refinement:
** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4899 r_free = 0.4899 target = 0.235799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.198788 restraints weight = 10500.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.202865 restraints weight = 7000.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.205516 restraints weight = 5436.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.207163 restraints weight = 4590.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.207844 restraints weight = 4137.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.4616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6021
moved from start:          0.5719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7602  Z= 0.146
  Angle     :  0.797  10.673  10360  Z= 0.404
  Chirality :  0.045   0.195   1204
  Planarity :  0.004   0.042   1298
  Dihedral  :  6.639  42.041   1048
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 11.93 %
    Favored  : 87.86 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.70 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.64 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.27), residues: 964
  helix:  0.14 (0.20), residues: 700
  sheet:  None (None), residues: 0
  loop : -4.50 (0.30), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 373 
 TYR   0.010   0.001   TYR A 338 
 PHE   0.023   0.002   PHE B 873 
 TRP   0.006   0.001   TRP B 305 
 HIS   0.004   0.001   HIS B 803 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7602)
  covalent geometry    : angle       0.79661 (10360)
  hydrogen bonds       : bond        0.04196 (  453)
  hydrogen bonds       : angle       4.70041 ( 1347)

********************** 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
  152 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  321 ARG cc_start: 0.5292 (tmt-80) cc_final: 0.2941 (ttm170)
REVERT: A  341 MET cc_start: 0.6852 (mtm) cc_final: 0.6576 (mtm)
REVERT: A  348 VAL cc_start: 0.7349 (m) cc_final: 0.7024 (t)
REVERT: A  351 ILE cc_start: 0.8372 (mt) cc_final: 0.8155 (mm)
REVERT: A  353 PHE cc_start: 0.6416 (OUTLIER) cc_final: 0.6003 (m-80)
REVERT: A  391 MET cc_start: 0.4634 (mpp) cc_final: 0.4190 (mpp)
REVERT: A  633 GLN cc_start: 0.4774 (mt0) cc_final: 0.4063 (mt0)
REVERT: A  638 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5781 (mmm)
REVERT: A  642 GLN cc_start: 0.6102 (mm110) cc_final: 0.5388 (mm110)
REVERT: B  321 ARG cc_start: 0.5335 (tmt-80) cc_final: 0.3204 (ttm170)
REVERT: B  341 MET cc_start: 0.6875 (mtm) cc_final: 0.6528 (mtm)
REVERT: B  353 PHE cc_start: 0.6320 (OUTLIER) cc_final: 0.5924 (m-10)
REVERT: B  391 MET cc_start: 0.3869 (mmt) cc_final: 0.2522 (ttt)
REVERT: B  574 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6186 (mm-30)
REVERT: B  633 GLN cc_start: 0.5120 (mt0) cc_final: 0.4793 (mt0)
REVERT: B  755 ILE cc_start: 0.6456 (mm) cc_final: 0.5872 (mt)
REVERT: B  797 MET cc_start: 0.2196 (mpp) cc_final: 0.1641 (mmt)
  outliers start: 17
  outliers final: 11
  residues processed: 140
  average time/residue: 0.0743
  time to fit residues: 14.8118
Evaluate side-chains
  140 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  353 PHE
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  638 MET
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  790 MET
Chi-restraints excluded: chain B residue  340 GLN
Chi-restraints excluded: chain B residue  353 PHE
Chi-restraints excluded: chain B residue  378 MET
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  785 LEU
Chi-restraints excluded: chain B residue  847 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 81 optimal weight:    0.0570
   chunk 29 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0030
   chunk 52 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0040
   chunk 14 optimal weight:    0.9980
   chunk 83 optimal weight:    0.2980
   chunk 7 optimal weight:    0.0060
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.0736

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

Flipped N/Q/H residues before XYZ refinement:
** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 815 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4935 r_free = 0.4935 target = 0.239413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.203512 restraints weight = 10477.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.206176 restraints weight = 7275.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.207675 restraints weight = 5754.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.207894 restraints weight = 5151.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.208268 restraints weight = 4972.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.4621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6007
moved from start:          0.6097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7602  Z= 0.142
  Angle     :  0.763  10.255  10360  Z= 0.391
  Chirality :  0.044   0.201   1204
  Planarity :  0.004   0.038   1298
  Dihedral  :  6.379  39.051   1048
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.14 %
    Favored  : 87.66 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 17.49 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.64 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.27), residues: 964
  helix:  0.29 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -4.49 (0.31), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 321 
 TYR   0.009   0.001   TYR B 338 
 PHE   0.022   0.002   PHE B 873 
 TRP   0.006   0.001   TRP A 427 
 HIS   0.005   0.001   HIS B 803 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7602)
  covalent geometry    : angle       0.76284 (10360)
  hydrogen bonds       : bond        0.03949 (  453)
  hydrogen bonds       : angle       4.62258 ( 1347)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1421.86 seconds
wall clock time: 25 minutes 14.64 seconds (1514.64 seconds total)