Starting phenix.real_space_refine
on Wed Feb  4 02:57:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9s3z_54556/02_2026/9s3z_54556.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9s3z_54556/02_2026/9s3z_54556.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9s3z_54556/02_2026/9s3z_54556.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9s3z_54556/02_2026/9s3z_54556.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9s3z_54556/02_2026/9s3z_54556.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9s3z_54556/02_2026/9s3z_54556.map"
  }
  resolution = 3.55
  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=   0.001 sd=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5335      2.51       5
     N    1399      2.21       5
     O    1565      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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8355
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2054
          Classifications: {'peptide': 268}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 257}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 78
          Unresolved non-hydrogen dihedrals: 58
          Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 6, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "B"
      Number of atoms: 2081
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2081
          Classifications: {'peptide': 276}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 264}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 100
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 43
    Chain: "C"
      Number of atoms: 2051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2051
          Classifications: {'peptide': 268}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 257}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 60
          Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 6, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 39
    Chain: "D"
      Number of atoms: 2077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2077
          Classifications: {'peptide': 275}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 263}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 100
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 7, 'ASP:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 43
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'E2Q': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'E2Q': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'E2Q': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'E2Q': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.08, per 1000 atoms: 0.25
  Number of scatterers: 8355
  At special positions: 0
  Unit cell: (119.77, 124.726, 85.904, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1565      8.00
     N    1399      7.00
     C    5335      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 714 " - pdb=" SG  CYS A 769 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 719 " - pdb=" SG  CYS B 774 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 714 " - pdb=" SG  CYS C 769 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 719 " - pdb=" SG  CYS D 774 " distance=2.03

  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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 317.6 milliseconds
  

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2004

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 19 sheets defined
      42.8% alpha, 16.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 407 through 411
    Processing helix  chain 'A' and resid 412 through 415
    Processing helix  chain 'A' and resid 419 through 433
    Processing helix  chain 'A' and resid 457 through 465
    Processing helix  chain 'A' and resid 478 through 483
    Processing helix  chain 'A' and resid 631 through 638
    Processing helix  chain 'A' and resid 649 through 658
    Processing helix  chain 'A' and resid 660 through 672
    Processing helix  chain 'A' and resid 681 through 693
      removed outlier: 3.914A  pdb=" N   LYS A 693 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 710
    Processing helix  chain 'A' and resid 738 through 752
    Processing helix  chain 'A' and resid 753 through 764
    Processing helix  chain 'B' and resid 417 through 420
    Processing helix  chain 'B' and resid 424 through 438
    Processing helix  chain 'B' and resid 462 through 470
    Processing helix  chain 'B' and resid 483 through 488
    Processing helix  chain 'B' and resid 636 through 643
    Processing helix  chain 'B' and resid 654 through 663
      removed outlier: 3.635A  pdb=" N   PHE B 660 " --> pdb=" O   THR B 656 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 665 through 678
      removed outlier: 3.503A  pdb=" N   TRP B 672 " --> pdb=" O   TYR B 668 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 686 through 697
    Processing helix  chain 'B' and resid 707 through 715
    Processing helix  chain 'B' and resid 743 through 757
    Processing helix  chain 'B' and resid 758 through 769
    Processing helix  chain 'C' and resid 407 through 411
    Processing helix  chain 'C' and resid 412 through 415
    Processing helix  chain 'C' and resid 419 through 433
    Processing helix  chain 'C' and resid 457 through 465
    Processing helix  chain 'C' and resid 478 through 483
    Processing helix  chain 'C' and resid 631 through 638
    Processing helix  chain 'C' and resid 649 through 658
    Processing helix  chain 'C' and resid 660 through 672
    Processing helix  chain 'C' and resid 681 through 693
      removed outlier: 4.053A  pdb=" N   LYS C 693 " --> pdb=" O   VAL C 689 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 702 through 710
    Processing helix  chain 'C' and resid 738 through 752
    Processing helix  chain 'C' and resid 753 through 764
    Processing helix  chain 'D' and resid 417 through 420
    Processing helix  chain 'D' and resid 424 through 438
    Processing helix  chain 'D' and resid 462 through 470
    Processing helix  chain 'D' and resid 483 through 488
    Processing helix  chain 'D' and resid 636 through 643
    Processing helix  chain 'D' and resid 653 through 663
      removed outlier: 4.368A  pdb=" N   LYS D 657 " --> pdb=" O   SER D 653 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLU D 658 " --> pdb=" O   GLY D 654 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 667 through 678
    Processing helix  chain 'D' and resid 686 through 697
    Processing helix  chain 'D' and resid 707 through 715
    Processing helix  chain 'D' and resid 743 through 757
    Processing helix  chain 'D' and resid 758 through 769
    Processing sheet with id=AA1, first strand: chain 'A' and resid 390 through 395
      removed outlier: 6.260A  pdb=" N   TYR A 391 " --> pdb=" O   ARG A 437 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   GLU A 439 " --> pdb=" O   TYR A 391 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   VAL A 393 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404
    Processing sheet with id=AA3, first strand: chain 'A' and resid 471 through 476
      removed outlier: 4.516A  pdb=" N   ALA A 473 " --> pdb=" O   GLY A 729 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   GLY A 729 " --> pdb=" O   ALA A 473 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   LEU A 475 " --> pdb=" O   GLY A 727 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   GLY A 727 " --> pdb=" O   LEU A 475 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 471 through 476
      removed outlier: 4.516A  pdb=" N   ALA A 473 " --> pdb=" O   GLY A 729 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   GLY A 729 " --> pdb=" O   ALA A 473 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   LEU A 475 " --> pdb=" O   GLY A 727 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   GLY A 727 " --> pdb=" O   LEU A 475 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   MET A 492 " --> pdb=" O   TYR A 728 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 642 through 644
      removed outlier: 6.773A  pdb=" N   ALA A 642 " --> pdb=" O   ALA A 697 " (cutoff:3.500A)
      removed outlier: 8.001A  pdb=" N   LEU A 699 " --> pdb=" O   ALA A 642 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   GLY A 644 " --> pdb=" O   LEU A 699 " (cutoff:3.500A)
      removed outlier: 9.217A  pdb=" N   GLU A 701 " --> pdb=" O   GLY A 644 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   TYR A 696 " --> pdb=" O   LYS A 501 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   LYS A 501 " --> pdb=" O   TYR A 696 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ILE A 498 " --> pdb=" O   VAL A 719 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 441 through 445
      removed outlier: 3.606A  pdb=" N   THR B 400 " --> pdb=" O   ALA B 444 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ILE B 475 " --> pdb=" O   VAL B 397 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE B 477 " --> pdb=" O   THR B 399 " (cutoff:3.500A)
      removed outlier: 9.675A  pdb=" N   ALA B 476 " --> pdb=" O   PRO B 738 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   ALA B 478 " --> pdb=" O   ALA B 736 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ALA B 736 " --> pdb=" O   ALA B 478 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   LEU B 480 " --> pdb=" O   GLY B 734 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 441 through 445
      removed outlier: 3.606A  pdb=" N   THR B 400 " --> pdb=" O   ALA B 444 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ILE B 475 " --> pdb=" O   VAL B 397 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE B 477 " --> pdb=" O   THR B 399 " (cutoff:3.500A)
      removed outlier: 9.675A  pdb=" N   ALA B 476 " --> pdb=" O   PRO B 738 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   ALA B 478 " --> pdb=" O   ALA B 736 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ALA B 736 " --> pdb=" O   ALA B 478 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   LEU B 480 " --> pdb=" O   GLY B 734 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   MET B 497 " --> pdb=" O   TYR B 733 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 408 through 409
    Processing sheet with id=AA9, first strand: chain 'B' and resid 647 through 649
      removed outlier: 8.646A  pdb=" N   PHE B 701 " --> pdb=" O   LYS B 506 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   LYS B 506 " --> pdb=" O   PHE B 701 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ILE B 503 " --> pdb=" O   VAL B 724 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 390 through 395
      removed outlier: 6.159A  pdb=" N   TYR C 391 " --> pdb=" O   ARG C 437 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLU C 439 " --> pdb=" O   TYR C 391 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   VAL C 393 " --> pdb=" O   GLU C 439 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'C' and resid 403 through 404
    Processing sheet with id=AB3, first strand: chain 'C' and resid 485 through 487
    Processing sheet with id=AB4, first strand: chain 'C' and resid 493 through 494
      removed outlier: 3.514A  pdb=" N   LYS C 726 " --> pdb=" O   LEU C 494 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 642 through 644
      removed outlier: 6.717A  pdb=" N   ALA C 642 " --> pdb=" O   ALA C 697 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   LEU C 699 " --> pdb=" O   ALA C 642 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   GLY C 644 " --> pdb=" O   LEU C 699 " (cutoff:3.500A)
      removed outlier: 9.187A  pdb=" N   GLU C 701 " --> pdb=" O   GLY C 644 " (cutoff:3.500A)
      removed outlier: 8.258A  pdb=" N   TYR C 696 " --> pdb=" O   LYS C 501 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   LYS C 501 " --> pdb=" O   TYR C 696 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ILE C 498 " --> pdb=" O   VAL C 719 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 395 through 400
      removed outlier: 3.518A  pdb=" N   THR D 400 " --> pdb=" O   ALA D 444 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 408 through 409
    Processing sheet with id=AB8, first strand: chain 'D' and resid 490 through 491
    Processing sheet with id=AB9, first strand: chain 'D' and resid 497 through 499
      removed outlier: 4.206A  pdb=" N   MET D 497 " --> pdb=" O   TYR D 733 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 647 through 649
      removed outlier: 6.666A  pdb=" N   ALA D 647 " --> pdb=" O   ALA D 702 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   LEU D 704 " --> pdb=" O   ALA D 647 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   GLY D 649 " --> pdb=" O   LEU D 704 " (cutoff:3.500A)
      removed outlier: 9.075A  pdb=" N   GLU D 706 " --> pdb=" O   GLY D 649 " (cutoff:3.500A)
      removed outlier: 8.581A  pdb=" N   PHE D 701 " --> pdb=" O   LYS D 506 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   LYS D 506 " --> pdb=" O   PHE D 701 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE D 503 " --> pdb=" O   VAL D 724 " (cutoff:3.500A)

    356 hydrogen bonds defined for protein.
    1014 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: 1.27

  Time building geometry restraints manager: 1.06 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1361
        1.30 -     1.43: 2231
        1.43 -     1.56: 4831
        1.56 -     1.70: 0
        1.70 -     1.83: 100
  Bond restraints: 8523
  Sorted by residual:
  bond pdb=" N15 E2Q D 901 "
       pdb=" O17 E2Q D 901 "
    ideal  model  delta    sigma   weight residual
    1.206  1.402 -0.196 2.00e-02 2.50e+03 9.56e+01
  bond pdb=" N15 E2Q C 901 "
       pdb=" O17 E2Q C 901 "
    ideal  model  delta    sigma   weight residual
    1.206  1.401 -0.195 2.00e-02 2.50e+03 9.54e+01
  bond pdb=" N15 E2Q B 901 "
       pdb=" O17 E2Q B 901 "
    ideal  model  delta    sigma   weight residual
    1.206  1.401 -0.195 2.00e-02 2.50e+03 9.47e+01
  bond pdb=" N15 E2Q A 901 "
       pdb=" O17 E2Q A 901 "
    ideal  model  delta    sigma   weight residual
    1.206  1.400 -0.194 2.00e-02 2.50e+03 9.45e+01
  bond pdb=" C04 E2Q C 901 "
       pdb=" N23 E2Q C 901 "
    ideal  model  delta    sigma   weight residual
    1.374  1.495 -0.121 2.00e-02 2.50e+03 3.65e+01
  ... (remaining 8518 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.15: 11468
        4.15 -     8.31: 63
        8.31 -    12.46: 6
       12.46 -    16.61: 4
       16.61 -    20.77: 12
  Bond angle restraints: 11553
  Sorted by residual:
  angle pdb=" O12 E2Q B 901 "
        pdb=" S11 E2Q B 901 "
        pdb=" O13 E2Q B 901 "
      ideal   model   delta    sigma   weight residual
     121.72  100.95   20.77 3.00e+00 1.11e-01 4.79e+01
  angle pdb=" O12 E2Q D 901 "
        pdb=" S11 E2Q D 901 "
        pdb=" O13 E2Q D 901 "
      ideal   model   delta    sigma   weight residual
     121.72  101.08   20.64 3.00e+00 1.11e-01 4.73e+01
  angle pdb=" O12 E2Q C 901 "
        pdb=" S11 E2Q C 901 "
        pdb=" O13 E2Q C 901 "
      ideal   model   delta    sigma   weight residual
     121.72  101.27   20.45 3.00e+00 1.11e-01 4.64e+01
  angle pdb=" O12 E2Q A 901 "
        pdb=" S11 E2Q A 901 "
        pdb=" O13 E2Q A 901 "
      ideal   model   delta    sigma   weight residual
     121.72  101.44   20.28 3.00e+00 1.11e-01 4.57e+01
  angle pdb=" C08 E2Q A 901 "
        pdb=" C07 E2Q A 901 "
        pdb=" N15 E2Q A 901 "
      ideal   model   delta    sigma   weight residual
     121.67  141.83  -20.16 3.00e+00 1.11e-01 4.51e+01
  ... (remaining 11548 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 4493
       17.82 -    35.64: 463
       35.64 -    53.46: 136
       53.46 -    71.27: 32
       71.27 -    89.09: 7
  Dihedral angle restraints: 5131
    sinusoidal: 1992
      harmonic: 3139
  Sorted by residual:
  dihedral pdb=" CB  CYS C 714 "
           pdb=" SG  CYS C 714 "
           pdb=" SG  CYS C 769 "
           pdb=" CB  CYS C 769 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.53  -63.53     1      1.00e+01 1.00e-02 5.32e+01
  dihedral pdb=" CB  CYS A 714 "
           pdb=" SG  CYS A 714 "
           pdb=" SG  CYS A 769 "
           pdb=" CB  CYS A 769 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.58  -60.58     1      1.00e+01 1.00e-02 4.89e+01
  dihedral pdb=" CB  CYS B 719 "
           pdb=" SG  CYS B 719 "
           pdb=" SG  CYS B 774 "
           pdb=" CB  CYS B 774 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.29  -43.29     1      1.00e+01 1.00e-02 2.61e+01
  ... (remaining 5128 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 676
       0.024 -    0.048: 324
       0.048 -    0.073: 160
       0.073 -    0.097: 74
       0.097 -    0.121: 58
  Chirality restraints: 1292
  Sorted by residual:
  chirality pdb=" CA  ILE B 646 "
            pdb=" N   ILE B 646 "
            pdb=" C   ILE B 646 "
            pdb=" CB  ILE B 646 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.65e-01
  chirality pdb=" CA  ILE B 634 "
            pdb=" N   ILE B 634 "
            pdb=" C   ILE B 634 "
            pdb=" CB  ILE B 634 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.61e-01
  chirality pdb=" CA  ILE D 634 "
            pdb=" N   ILE D 634 "
            pdb=" C   ILE D 634 "
            pdb=" CB  ILE D 634 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.60e-01
  ... (remaining 1289 not shown)

  Planarity restraints: 1450
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 399 "   -0.043 5.00e-02 4.00e+02   6.45e-02 6.66e+00
        pdb=" N   PRO A 400 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 400 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 400 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 674 "    0.037 5.00e-02 4.00e+02   5.53e-02 4.89e+00
        pdb=" N   PRO C 675 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO C 675 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C 675 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 674 "   -0.031 5.00e-02 4.00e+02   4.75e-02 3.61e+00
        pdb=" N   PRO A 675 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 675 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 675 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1447 not shown)

  Histogram of nonbonded interaction distances:
        2.48 -     2.97: 3872
        2.97 -     3.45: 8061
        3.45 -     3.93: 13397
        3.93 -     4.42: 14581
        4.42 -     4.90: 25007
  Nonbonded interactions: 64918
  Sorted by model distance:
  nonbonded pdb=" N   GLU D 392 "
            pdb=" OE1 GLU D 392 "
     model   vdw
     2.483 3.120
  nonbonded pdb=" N   GLN D 509 "
            pdb=" OE1 GLN D 509 "
     model   vdw
     2.521 3.120
  nonbonded pdb=" N   ASP A 715 "
            pdb=" OD1 ASP A 715 "
     model   vdw
     2.559 3.120
  nonbonded pdb=" OD1 ASN C 409 "
            pdb=" OE1 GLN C 410 "
     model   vdw
     2.581 3.040
  nonbonded pdb=" N   GLU A 623 "
            pdb=" OE1 GLU A 623 "
     model   vdw
     2.589 3.120
  ... (remaining 64913 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 386 through 679 or (resid 680 and (name N or name CA or na \ 
me C or name O or name CB or name CG or name CD or name NE )) or resid 681 throu \ 
gh 901))
  selection = chain 'C'
}
ncs_group {
  reference = (chain 'B' and (resid 391 through 466 or (resid 467 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 468 through 513 or resid 624 through 901)) \ 

  selection = (chain 'D' and (resid 391 or (resid 392 through 393 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 394 through 901))
}

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:             7.930
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.000
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
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      :  0.007   0.196   8530  Z= 0.341
  Angle     :  0.970  20.766  11561  Z= 0.393
  Chirality :  0.042   0.121   1292
  Planarity :  0.004   0.065   1450
  Dihedral  : 16.074  89.092   3115
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 19.98 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.26), residues: 1071
  helix:  0.90 (0.25), residues: 438
  sheet: -1.31 (0.43), residues: 133
  loop : -0.09 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 454 
 TYR   0.011   0.001   TYR D 406 
 PHE   0.016   0.001   PHE C 655 
 TRP   0.017   0.001   TRP D 767 
 HIS   0.001   0.000   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00690 ( 8523)
  covalent geometry    : angle       0.96982 (11553)
  SS BOND              : bond        0.00183 (    4)
  SS BOND              : angle       1.07258 (    8)
  hydrogen bonds       : bond        0.18380 (  349)
  hydrogen bonds       : angle       7.10098 ( 1014)
  Misc. bond           : bond        0.00128 (    3)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 174
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  416 PHE cc_start: 0.6503 (m-80) cc_final: 0.6255 (m-80)
REVERT: B  442 LYS cc_start: 0.7737 (tttt) cc_final: 0.7398 (pttt)
REVERT: B  720 ASP cc_start: 0.7150 (p0) cc_final: 0.6865 (p0)
REVERT: D  428 ASP cc_start: 0.7861 (m-30) cc_final: 0.7624 (m-30)
REVERT: D  432 GLU cc_start: 0.7668 (mp0) cc_final: 0.7319 (mp0)
REVERT: D  435 LYS cc_start: 0.8083 (tmtt) cc_final: 0.7756 (ttmm)
REVERT: D  442 LYS cc_start: 0.7749 (tttt) cc_final: 0.7467 (pttt)
REVERT: D  455 ASP cc_start: 0.6104 (t70) cc_final: 0.5845 (t70)
REVERT: D  458 THR cc_start: 0.8527 (t) cc_final: 0.8272 (t)
REVERT: D  487 GLU cc_start: 0.7941 (tp30) cc_final: 0.7733 (mm-30)
REVERT: D  720 ASP cc_start: 0.7569 (p0) cc_final: 0.7340 (p0)
REVERT: D  762 LYS cc_start: 0.8693 (tppt) cc_final: 0.8407 (tmmt)
  outliers start: 3
  outliers final: 3
  residues processed: 177
  average time/residue: 0.0795
  time to fit residues: 19.9746
Evaluate side-chains
  147 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 144
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  394 ARG
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain D residue  401 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0170
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
A 638 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.157213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.130177 restraints weight = 12012.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.130781 restraints weight = 9859.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.131409 restraints weight = 10182.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.132457 restraints weight = 6556.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.133033 restraints weight = 5852.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8530  Z= 0.123
  Angle     :  0.547   8.050  11561  Z= 0.269
  Chirality :  0.042   0.128   1292
  Planarity :  0.004   0.048   1450
  Dihedral  :  8.236  59.960   1246
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 18.79 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.26), residues: 1071
  helix:  1.14 (0.25), residues: 439
  sheet: -1.17 (0.42), residues: 145
  loop : -0.07 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 481 
 TYR   0.010   0.001   TYR B 406 
 PHE   0.013   0.001   PHE D 496 
 TRP   0.016   0.001   TRP D 767 
 HIS   0.002   0.001   HIS D 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8523)
  covalent geometry    : angle       0.54658 (11553)
  SS BOND              : bond        0.00527 (    4)
  SS BOND              : angle       0.79082 (    8)
  hydrogen bonds       : bond        0.03440 (  349)
  hydrogen bonds       : angle       5.29795 ( 1014)
  Misc. bond           : bond        0.00067 (    3)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 156
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  501 LYS cc_start: 0.8444 (tttt) cc_final: 0.8241 (tttt)
REVERT: B  442 LYS cc_start: 0.7598 (tttt) cc_final: 0.7316 (pttt)
REVERT: B  720 ASP cc_start: 0.7056 (p0) cc_final: 0.6671 (p0)
REVERT: D  428 ASP cc_start: 0.8084 (m-30) cc_final: 0.7792 (m-30)
REVERT: D  432 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7241 (mp0)
REVERT: D  442 LYS cc_start: 0.7664 (tttt) cc_final: 0.7325 (pttt)
REVERT: D  662 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7574 (mtm-85)
REVERT: D  720 ASP cc_start: 0.7239 (p0) cc_final: 0.6959 (p0)
  outliers start: 23
  outliers final: 13
  residues processed: 170
  average time/residue: 0.0785
  time to fit residues: 18.9387
Evaluate side-chains
  154 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain B residue  394 ARG
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  694 VAL
Chi-restraints excluded: chain B residue  773 GLU
Chi-restraints excluded: chain C residue  394 THR
Chi-restraints excluded: chain C residue  622 VAL
Chi-restraints excluded: chain C residue  623 GLU
Chi-restraints excluded: chain C residue  679 VAL
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain D residue  401 ILE
Chi-restraints excluded: chain D residue  432 GLU
Chi-restraints excluded: chain D residue  774 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 638 GLN
** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 638 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.156660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.130133 restraints weight = 11923.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.129841 restraints weight = 10246.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.130789 restraints weight = 11357.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.131911 restraints weight = 7343.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.132447 restraints weight = 6503.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8530  Z= 0.197
  Angle     :  0.596   7.512  11561  Z= 0.297
  Chirality :  0.044   0.157   1292
  Planarity :  0.004   0.038   1450
  Dihedral  :  8.218  59.737   1246
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 19.98 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.25), residues: 1071
  helix:  1.00 (0.25), residues: 438
  sheet: -1.58 (0.40), residues: 150
  loop : -0.13 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 481 
 TYR   0.015   0.002   TYR A 420 
 PHE   0.023   0.002   PHE C 491 
 TRP   0.017   0.002   TRP D 767 
 HIS   0.004   0.001   HIS B 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 8523)
  covalent geometry    : angle       0.59518 (11553)
  SS BOND              : bond        0.00392 (    4)
  SS BOND              : angle       1.26121 (    8)
  hydrogen bonds       : bond        0.03601 (  349)
  hydrogen bonds       : angle       5.20296 ( 1014)
  Misc. bond           : bond        0.00103 (    3)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 153
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  442 LYS cc_start: 0.7573 (tttt) cc_final: 0.7246 (pttt)
REVERT: B  720 ASP cc_start: 0.7205 (p0) cc_final: 0.6871 (p0)
REVERT: C  452 ASP cc_start: 0.8076 (p0) cc_final: 0.7863 (p0)
REVERT: C  462 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6700 (mt-10)
REVERT: D  428 ASP cc_start: 0.8289 (m-30) cc_final: 0.8080 (m-30)
REVERT: D  432 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7350 (mp0)
REVERT: D  442 LYS cc_start: 0.7626 (tttt) cc_final: 0.7252 (pttt)
REVERT: D  720 ASP cc_start: 0.7302 (p0) cc_final: 0.7022 (p0)
  outliers start: 32
  outliers final: 19
  residues processed: 173
  average time/residue: 0.0683
  time to fit residues: 17.5140
Evaluate side-chains
  164 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  686 MET
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain B residue  394 ARG
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain B residue  694 VAL
Chi-restraints excluded: chain B residue  773 GLU
Chi-restraints excluded: chain C residue  394 THR
Chi-restraints excluded: chain C residue  462 GLU
Chi-restraints excluded: chain C residue  622 VAL
Chi-restraints excluded: chain C residue  623 GLU
Chi-restraints excluded: chain C residue  626 VAL
Chi-restraints excluded: chain C residue  679 VAL
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain D residue  401 ILE
Chi-restraints excluded: chain D residue  432 GLU
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain D residue  694 VAL
Chi-restraints excluded: chain D residue  774 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 105 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 81 optimal weight:    8.9990
   chunk 85 optimal weight:    0.2980
   chunk 63 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 638 GLN
** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 638 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.158120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.131065 restraints weight = 12084.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.130400 restraints weight = 10042.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.131579 restraints weight = 10162.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.132492 restraints weight = 7176.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.132903 restraints weight = 7027.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8530  Z= 0.144
  Angle     :  0.557   8.666  11561  Z= 0.275
  Chirality :  0.042   0.126   1292
  Planarity :  0.004   0.034   1450
  Dihedral  :  7.924  59.679   1246
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.24 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.25), residues: 1071
  helix:  1.14 (0.25), residues: 438
  sheet: -1.56 (0.40), residues: 150
  loop : -0.12 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 481 
 TYR   0.014   0.001   TYR A 669 
 PHE   0.013   0.001   PHE B 496 
 TRP   0.017   0.001   TRP D 767 
 HIS   0.002   0.001   HIS D 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8523)
  covalent geometry    : angle       0.55622 (11553)
  SS BOND              : bond        0.00212 (    4)
  SS BOND              : angle       1.16575 (    8)
  hydrogen bonds       : bond        0.03088 (  349)
  hydrogen bonds       : angle       4.97202 ( 1014)
  Misc. bond           : bond        0.00082 (    3)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 147
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  651 LEU cc_start: 0.8552 (tt) cc_final: 0.8162 (mt)
REVERT: B  720 ASP cc_start: 0.7225 (p0) cc_final: 0.6901 (p0)
REVERT: C  452 ASP cc_start: 0.8154 (p0) cc_final: 0.7908 (p0)
REVERT: D  428 ASP cc_start: 0.8373 (m-30) cc_final: 0.8146 (m-30)
REVERT: D  432 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7277 (mp0)
REVERT: D  442 LYS cc_start: 0.7622 (tttt) cc_final: 0.7247 (pttt)
REVERT: D  720 ASP cc_start: 0.7255 (p0) cc_final: 0.7010 (p0)
  outliers start: 25
  outliers final: 19
  residues processed: 163
  average time/residue: 0.0722
  time to fit residues: 17.3358
Evaluate side-chains
  159 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain B residue  394 ARG
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  694 VAL
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  773 GLU
Chi-restraints excluded: chain C residue  394 THR
Chi-restraints excluded: chain C residue  622 VAL
Chi-restraints excluded: chain C residue  623 GLU
Chi-restraints excluded: chain C residue  626 VAL
Chi-restraints excluded: chain C residue  679 VAL
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain D residue  401 ILE
Chi-restraints excluded: chain D residue  432 GLU
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain D residue  694 VAL
Chi-restraints excluded: chain D residue  774 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 62 optimal weight:    0.4980
   chunk 78 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 67 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 410 GLN
C 638 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.158037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.130949 restraints weight = 12072.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.131373 restraints weight = 9675.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.132058 restraints weight = 10519.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.133331 restraints weight = 6663.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.134327 restraints weight = 5794.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8530  Z= 0.139
  Angle     :  0.544   6.648  11561  Z= 0.270
  Chirality :  0.042   0.123   1292
  Planarity :  0.004   0.037   1450
  Dihedral  :  7.594  56.295   1246
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 22.00 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.25), residues: 1071
  helix:  1.25 (0.25), residues: 438
  sheet: -1.55 (0.39), residues: 157
  loop : -0.18 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 481 
 TYR   0.013   0.001   TYR A 728 
 PHE   0.013   0.001   PHE C 491 
 TRP   0.018   0.001   TRP D 767 
 HIS   0.002   0.001   HIS B 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8523)
  covalent geometry    : angle       0.54350 (11553)
  SS BOND              : bond        0.00227 (    4)
  SS BOND              : angle       1.07873 (    8)
  hydrogen bonds       : bond        0.02993 (  349)
  hydrogen bonds       : angle       4.87394 ( 1014)
  Misc. bond           : bond        0.00081 (    3)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 146
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: B  651 LEU cc_start: 0.8597 (tt) cc_final: 0.8183 (mt)
REVERT: B  720 ASP cc_start: 0.7252 (p0) cc_final: 0.6919 (p0)
REVERT: C  452 ASP cc_start: 0.8128 (p0) cc_final: 0.7880 (p0)
REVERT: D  428 ASP cc_start: 0.8391 (m-30) cc_final: 0.8086 (m-30)
REVERT: D  432 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7263 (mp0)
REVERT: D  487 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7438 (mm-30)
REVERT: D  720 ASP cc_start: 0.7296 (p0) cc_final: 0.7045 (p0)
  outliers start: 27
  outliers final: 19
  residues processed: 165
  average time/residue: 0.0728
  time to fit residues: 17.2520
Evaluate side-chains
  163 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain B residue  394 ARG
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain B residue  694 VAL
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  773 GLU
Chi-restraints excluded: chain C residue  394 THR
Chi-restraints excluded: chain C residue  622 VAL
Chi-restraints excluded: chain C residue  623 GLU
Chi-restraints excluded: chain C residue  626 VAL
Chi-restraints excluded: chain C residue  679 VAL
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain D residue  401 ILE
Chi-restraints excluded: chain D residue  432 GLU
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain D residue  694 VAL
Chi-restraints excluded: chain D residue  774 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 0 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 638 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.156698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.131267 restraints weight = 11915.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.131388 restraints weight = 11633.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.132804 restraints weight = 10089.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.133540 restraints weight = 7118.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.134069 restraints weight = 7083.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8530  Z= 0.155
  Angle     :  0.554   8.949  11561  Z= 0.274
  Chirality :  0.042   0.122   1292
  Planarity :  0.004   0.036   1450
  Dihedral  :  7.420  54.400   1246
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 23.31 %
    Favored  : 73.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.25), residues: 1071
  helix:  1.25 (0.25), residues: 438
  sheet: -1.60 (0.40), residues: 150
  loop : -0.12 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 481 
 TYR   0.013   0.001   TYR A 728 
 PHE   0.015   0.002   PHE C 491 
 TRP   0.018   0.001   TRP D 767 
 HIS   0.002   0.001   HIS B 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 8523)
  covalent geometry    : angle       0.55347 (11553)
  SS BOND              : bond        0.00091 (    4)
  SS BOND              : angle       1.06913 (    8)
  hydrogen bonds       : bond        0.03014 (  349)
  hydrogen bonds       : angle       4.88799 ( 1014)
  Misc. bond           : bond        0.00098 (    3)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 148
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: B  432 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7072 (mp0)
REVERT: B  651 LEU cc_start: 0.8591 (tt) cc_final: 0.8131 (mt)
REVERT: B  720 ASP cc_start: 0.7188 (p0) cc_final: 0.6857 (p0)
REVERT: C  452 ASP cc_start: 0.7943 (p0) cc_final: 0.7700 (p0)
REVERT: D  428 ASP cc_start: 0.8371 (m-30) cc_final: 0.8115 (m-30)
REVERT: D  432 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7303 (mp0)
REVERT: D  487 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7520 (mm-30)
REVERT: D  720 ASP cc_start: 0.7236 (p0) cc_final: 0.6967 (p0)
  outliers start: 29
  outliers final: 21
  residues processed: 168
  average time/residue: 0.0729
  time to fit residues: 17.6596
Evaluate side-chains
  161 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain B residue  394 ARG
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  432 GLU
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain B residue  694 VAL
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  773 GLU
Chi-restraints excluded: chain C residue  394 THR
Chi-restraints excluded: chain C residue  499 MET
Chi-restraints excluded: chain C residue  622 VAL
Chi-restraints excluded: chain C residue  623 GLU
Chi-restraints excluded: chain C residue  626 VAL
Chi-restraints excluded: chain C residue  679 VAL
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain D residue  401 ILE
Chi-restraints excluded: chain D residue  404 SER
Chi-restraints excluded: chain D residue  432 GLU
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain D residue  694 VAL
Chi-restraints excluded: chain D residue  774 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 55 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0070
   chunk 26 optimal weight:    0.0770
   chunk 82 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A 638 GLN
** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 638 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.159599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.132488 restraints weight = 12051.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.132673 restraints weight = 10221.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.133828 restraints weight = 10384.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.134951 restraints weight = 6657.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.135388 restraints weight = 5912.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8530  Z= 0.115
  Angle     :  0.527   8.978  11561  Z= 0.261
  Chirality :  0.042   0.122   1292
  Planarity :  0.003   0.038   1450
  Dihedral  :  7.058  53.090   1246
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 23.78 %
    Favored  : 73.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.26), residues: 1071
  helix:  1.43 (0.25), residues: 438
  sheet: -1.38 (0.38), residues: 160
  loop : -0.11 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 481 
 TYR   0.013   0.001   TYR D 451 
 PHE   0.013   0.001   PHE B 496 
 TRP   0.020   0.001   TRP D 767 
 HIS   0.001   0.000   HIS B 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8523)
  covalent geometry    : angle       0.52709 (11553)
  SS BOND              : bond        0.00073 (    4)
  SS BOND              : angle       0.83879 (    8)
  hydrogen bonds       : bond        0.02708 (  349)
  hydrogen bonds       : angle       4.75390 ( 1014)
  Misc. bond           : bond        0.00082 (    3)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 147
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: B  432 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6927 (mp0)
REVERT: B  509 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8252 (pm20)
REVERT: B  651 LEU cc_start: 0.8573 (tt) cc_final: 0.8143 (mt)
REVERT: B  720 ASP cc_start: 0.7238 (p0) cc_final: 0.6890 (p0)
REVERT: C  452 ASP cc_start: 0.8104 (p0) cc_final: 0.7846 (p0)
REVERT: D  428 ASP cc_start: 0.8403 (m-30) cc_final: 0.8148 (m-30)
REVERT: D  432 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7247 (mp0)
REVERT: D  487 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7492 (mm-30)
REVERT: D  720 ASP cc_start: 0.7276 (p0) cc_final: 0.6959 (p0)
  outliers start: 25
  outliers final: 15
  residues processed: 163
  average time/residue: 0.0702
  time to fit residues: 16.7641
Evaluate side-chains
  163 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain B residue  394 ARG
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  432 GLU
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain B residue  509 GLN
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  773 GLU
Chi-restraints excluded: chain C residue  394 THR
Chi-restraints excluded: chain C residue  623 GLU
Chi-restraints excluded: chain C residue  679 VAL
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain D residue  401 ILE
Chi-restraints excluded: chain D residue  404 SER
Chi-restraints excluded: chain D residue  432 GLU
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain D residue  774 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0670
   chunk 12 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 2 optimal weight:    0.3980
   chunk 72 optimal weight:    1.9990
   chunk 3 optimal weight:    0.3980
   chunk 64 optimal weight:    0.7980
   chunk 71 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
A 638 GLN
** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 638 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.158119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.131783 restraints weight = 11838.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.132304 restraints weight = 10146.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.133533 restraints weight = 9847.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.134329 restraints weight = 6662.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.134744 restraints weight = 6526.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8530  Z= 0.111
  Angle     :  0.530   9.942  11561  Z= 0.260
  Chirality :  0.041   0.120   1292
  Planarity :  0.003   0.038   1450
  Dihedral  :  6.817  53.087   1246
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 24.26 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.26), residues: 1071
  helix:  1.49 (0.25), residues: 438
  sheet: -1.29 (0.39), residues: 160
  loop : -0.08 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 481 
 TYR   0.013   0.001   TYR D 406 
 PHE   0.012   0.001   PHE B 496 
 TRP   0.021   0.001   TRP D 767 
 HIS   0.001   0.000   HIS D 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8523)
  covalent geometry    : angle       0.52939 (11553)
  SS BOND              : bond        0.00105 (    4)
  SS BOND              : angle       0.87986 (    8)
  hydrogen bonds       : bond        0.02653 (  349)
  hydrogen bonds       : angle       4.70265 ( 1014)
  Misc. bond           : bond        0.00076 (    3)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 154
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  638 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.8015 (tm-30)
REVERT: B  509 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8303 (pm20)
REVERT: B  651 LEU cc_start: 0.8599 (tt) cc_final: 0.8153 (mt)
REVERT: B  720 ASP cc_start: 0.7202 (p0) cc_final: 0.6859 (p0)
REVERT: D  428 ASP cc_start: 0.8374 (m-30) cc_final: 0.8137 (m-30)
REVERT: D  432 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7238 (mp0)
REVERT: D  487 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7376 (mm-30)
REVERT: D  720 ASP cc_start: 0.7241 (p0) cc_final: 0.6918 (p0)
  outliers start: 22
  outliers final: 17
  residues processed: 167
  average time/residue: 0.0637
  time to fit residues: 15.8798
Evaluate side-chains
  165 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  387 GLN
Chi-restraints excluded: chain A residue  638 GLN
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain B residue  394 ARG
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain B residue  509 GLN
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  773 GLU
Chi-restraints excluded: chain C residue  623 GLU
Chi-restraints excluded: chain C residue  626 VAL
Chi-restraints excluded: chain C residue  679 VAL
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain D residue  401 ILE
Chi-restraints excluded: chain D residue  404 SER
Chi-restraints excluded: chain D residue  432 GLU
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain D residue  774 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   chunk 101 optimal weight:    1.9990
   chunk 75 optimal weight:    0.4980
   chunk 50 optimal weight:    0.0670
   chunk 45 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.158163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.132126 restraints weight = 11802.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.132165 restraints weight = 10412.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.134482 restraints weight = 8817.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.134550 restraints weight = 6399.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.134908 restraints weight = 6367.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8530  Z= 0.124
  Angle     :  0.544  10.498  11561  Z= 0.267
  Chirality :  0.042   0.135   1292
  Planarity :  0.003   0.039   1450
  Dihedral  :  6.793  53.124   1246
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 24.49 %
    Favored  : 73.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.25), residues: 1071
  helix:  1.47 (0.25), residues: 438
  sheet: -1.32 (0.38), residues: 160
  loop : -0.10 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 680 
 TYR   0.012   0.001   TYR D 451 
 PHE   0.013   0.001   PHE B 496 
 TRP   0.021   0.001   TRP D 767 
 HIS   0.002   0.000   HIS D 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8523)
  covalent geometry    : angle       0.54341 (11553)
  SS BOND              : bond        0.00088 (    4)
  SS BOND              : angle       0.95222 (    8)
  hydrogen bonds       : bond        0.02699 (  349)
  hydrogen bonds       : angle       4.73991 ( 1014)
  Misc. bond           : bond        0.00080 (    3)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 149
  time to evaluate  : 0.318 
Fit side-chains
REVERT: B  432 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6920 (mp0)
REVERT: B  509 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8301 (pm20)
REVERT: B  651 LEU cc_start: 0.8548 (tt) cc_final: 0.8131 (mt)
REVERT: B  720 ASP cc_start: 0.7185 (p0) cc_final: 0.6836 (p0)
REVERT: D  428 ASP cc_start: 0.8355 (m-30) cc_final: 0.8109 (m-30)
REVERT: D  432 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7249 (mp0)
REVERT: D  487 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7365 (mm-30)
REVERT: D  720 ASP cc_start: 0.7209 (p0) cc_final: 0.6892 (p0)
  outliers start: 21
  outliers final: 17
  residues processed: 162
  average time/residue: 0.0638
  time to fit residues: 15.5503
Evaluate side-chains
  165 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  387 GLN
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain B residue  394 ARG
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  432 GLU
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain B residue  497 MET
Chi-restraints excluded: chain B residue  509 GLN
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  773 GLU
Chi-restraints excluded: chain C residue  623 GLU
Chi-restraints excluded: chain C residue  626 VAL
Chi-restraints excluded: chain C residue  679 VAL
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain D residue  401 ILE
Chi-restraints excluded: chain D residue  404 SER
Chi-restraints excluded: chain D residue  432 GLU
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain D residue  774 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 31 optimal weight:    0.0060
   chunk 84 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 30 optimal weight:    0.4980
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 638 GLN
** D 643 GLN ** 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 = 0.3896 r_free = 0.3896 target = 0.160121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.133512 restraints weight = 11900.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.133426 restraints weight = 10168.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.135646 restraints weight = 8851.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.135780 restraints weight = 6373.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.136153 restraints weight = 6512.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8530  Z= 0.121
  Angle     :  0.543  11.345  11561  Z= 0.266
  Chirality :  0.042   0.126   1292
  Planarity :  0.003   0.038   1450
  Dihedral  :  6.733  53.375   1246
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 24.85 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.26), residues: 1071
  helix:  1.48 (0.25), residues: 438
  sheet: -1.31 (0.38), residues: 160
  loop : -0.08 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 680 
 TYR   0.012   0.001   TYR A 728 
 PHE   0.013   0.001   PHE B 496 
 TRP   0.021   0.001   TRP D 767 
 HIS   0.002   0.000   HIS D 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8523)
  covalent geometry    : angle       0.54292 (11553)
  SS BOND              : bond        0.00086 (    4)
  SS BOND              : angle       0.93057 (    8)
  hydrogen bonds       : bond        0.02676 (  349)
  hydrogen bonds       : angle       4.73664 ( 1014)
  Misc. bond           : bond        0.00087 (    3)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.213 
Fit side-chains
REVERT: B  432 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6897 (mp0)
REVERT: B  651 LEU cc_start: 0.8577 (tt) cc_final: 0.8168 (mt)
REVERT: B  720 ASP cc_start: 0.7198 (p0) cc_final: 0.6837 (p0)
REVERT: D  428 ASP cc_start: 0.8408 (m-30) cc_final: 0.8146 (m-30)
REVERT: D  432 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7230 (mp0)
REVERT: D  487 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7379 (mm-30)
REVERT: D  720 ASP cc_start: 0.7254 (p0) cc_final: 0.6939 (p0)
  outliers start: 20
  outliers final: 16
  residues processed: 161
  average time/residue: 0.0599
  time to fit residues: 14.3810
Evaluate side-chains
  160 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  387 GLN
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain B residue  394 ARG
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  432 GLU
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain B residue  497 MET
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  773 GLU
Chi-restraints excluded: chain C residue  626 VAL
Chi-restraints excluded: chain C residue  679 VAL
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain D residue  401 ILE
Chi-restraints excluded: chain D residue  432 GLU
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain D residue  774 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0170
   chunk 45 optimal weight:    0.0970
   chunk 77 optimal weight:    0.9990
   chunk 76 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 60 optimal weight:    0.4980
   chunk 46 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.3816

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

Flipped N/Q/H residues before XYZ refinement:
** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 638 GLN
** D 643 GLN ** 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 = 0.3889 r_free = 0.3889 target = 0.159121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.133336 restraints weight = 11854.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.133707 restraints weight = 10351.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.136434 restraints weight = 8755.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.136587 restraints weight = 6054.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.136903 restraints weight = 5786.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8530  Z= 0.108
  Angle     :  0.541  11.460  11561  Z= 0.266
  Chirality :  0.042   0.127   1292
  Planarity :  0.003   0.038   1450
  Dihedral  :  6.677  53.825   1246
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 24.85 %
    Favored  : 73.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.26), residues: 1071
  helix:  1.54 (0.25), residues: 438
  sheet: -1.27 (0.39), residues: 160
  loop : -0.02 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 680 
 TYR   0.012   0.001   TYR C 669 
 PHE   0.012   0.001   PHE B 496 
 TRP   0.019   0.001   TRP D 767 
 HIS   0.001   0.000   HIS D 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8523)
  covalent geometry    : angle       0.54098 (11553)
  SS BOND              : bond        0.00089 (    4)
  SS BOND              : angle       0.78625 (    8)
  hydrogen bonds       : bond        0.02582 (  349)
  hydrogen bonds       : angle       4.68713 ( 1014)
  Misc. bond           : bond        0.00076 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1378.57 seconds
wall clock time: 24 minutes 31.11 seconds (1471.11 seconds total)