Starting phenix.real_space_refine
on Sun Apr  5 12:28:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m8u_63722/04_2026/9m8u_63722.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m8u_63722/04_2026/9m8u_63722.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m8u_63722/04_2026/9m8u_63722.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m8u_63722/04_2026/9m8u_63722.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m8u_63722/04_2026/9m8u_63722.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m8u_63722/04_2026/9m8u_63722.map"
  }
  resolution = 3.79
  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=   0.003 sd=   0.066
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      60      5.16       5
     C    6704      2.51       5
     N    1606      2.21       5
     O    1748      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10118
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 624, 5059
          Classifications: {'peptide': 624}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 601}
          Chain breaks: 4
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.44, per 1000 atoms: 0.34
  Number of scatterers: 10118
  At special positions: 0
  Unit cell: (86.9, 102.3, 133.1, 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      60     16.00
     O    1748      8.00
     N    1606      7.00
     C    6704      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 130 " - pdb=" SG  CYS A 222 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 212 " - pdb=" SG  CYS A 271 " distance=2.00
    Simple disulfide: pdb=" SG  CYS A 479 " - pdb=" SG  CYS A 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 130 " - pdb=" SG  CYS B 222 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 212 " - pdb=" SG  CYS B 271 " distance=2.00
    Simple disulfide: pdb=" SG  CYS B 479 " - pdb=" SG  CYS B 565 " 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=0, symmetry=0
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 489.2 milliseconds
  

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2388

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 8 sheets defined
      43.9% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 114 through 118
      removed outlier: 4.119A  pdb=" N   GLN A 117 " --> pdb=" O   GLY A 114 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ARG A 118 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 114 through 118'
    Processing helix  chain 'A' and resid 302 through 316
      removed outlier: 4.147A  pdb=" N   TYR A 306 " --> pdb=" O   LYS A 302 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LEU A 311 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   VAL A 314 " --> pdb=" O   SER A 310 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 336
      removed outlier: 3.769A  pdb=" N   TYR A 321 " --> pdb=" O   PHE A 317 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   CYS A 324 " --> pdb=" O   PHE A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 473
      removed outlier: 4.202A  pdb=" N   ILE A 448 " --> pdb=" O   TYR A 444 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   PHE A 454 " --> pdb=" O   THR A 450 " (cutoff:3.500A)
      Proline residue:  A 458  - end of helix
      removed outlier: 3.751A  pdb=" N   GLN A 461 " --> pdb=" O   LEU A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 501
    Processing helix  chain 'A' and resid 502 through 524
      removed outlier: 3.575A  pdb=" N   LEU A 507 " --> pdb=" O   GLY A 503 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU A 510 " --> pdb=" O   LEU A 506 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   PHE A 511 " --> pdb=" O   LEU A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 561
      removed outlier: 4.201A  pdb=" N   LEU A 552 " --> pdb=" O   MET A 548 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLY A 556 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 577
    Processing helix  chain 'A' and resid 577 through 591
    Processing helix  chain 'A' and resid 609 through 619
      removed outlier: 3.786A  pdb=" N   THR A 615 " --> pdb=" O   VAL A 611 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   VAL A 616 " --> pdb=" O   ILE A 612 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   VAL A 619 " --> pdb=" O   THR A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 644
      removed outlier: 4.088A  pdb=" N   VAL A 630 " --> pdb=" O   VAL A 626 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ALA A 634 " --> pdb=" O   VAL A 630 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL A 637 " --> pdb=" O   SER A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 705
      removed outlier: 3.524A  pdb=" N   VAL A 698 " --> pdb=" O   VAL A 694 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   ASN A 699 " --> pdb=" O   GLY A 695 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU A 704 " --> pdb=" O   TRP A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 708
      No H-bonds generated for 'chain 'A' and resid 706 through 708'
    Processing helix  chain 'A' and resid 716 through 740
      removed outlier: 3.809A  pdb=" N   PHE A 722 " --> pdb=" O   MET A 718 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ILE A 723 " --> pdb=" O   LEU A 719 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   CYS A 724 " --> pdb=" O   GLY A 720 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU A 728 " --> pdb=" O   CYS A 724 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   SER A 740 " --> pdb=" O   MET A 736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 767
      removed outlier: 3.862A  pdb=" N   LEU A 749 " --> pdb=" O   LEU A 745 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   CYS A 751 " --> pdb=" O   VAL A 747 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA A 756 " --> pdb=" O   ILE A 752 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   VAL A 757 " --> pdb=" O   VAL A 753 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   MET A 758 " --> pdb=" O   ALA A 754 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   TYR A 764 " --> pdb=" O   ALA A 760 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   PHE A 765 " --> pdb=" O   ALA A 761 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   PHE A 767 " --> pdb=" O   LEU A 763 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 778 through 782
    Processing helix  chain 'A' and resid 796 through 817
      removed outlier: 3.586A  pdb=" N   HIS A 800 " --> pdb=" O   HIS A 796 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU A 802 " --> pdb=" O   ILE A 798 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA A 804 " --> pdb=" O   HIS A 800 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ALA A 806 " --> pdb=" O   LEU A 802 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU A 812 " --> pdb=" O   PHE A 808 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   VAL A 813 " --> pdb=" O   PHE A 809 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU A 814 " --> pdb=" O   SER A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 825
    Processing helix  chain 'B' and resid 114 through 118
      removed outlier: 4.119A  pdb=" N   GLN B 117 " --> pdb=" O   GLY B 114 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ARG B 118 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 114 through 118'
    Processing helix  chain 'B' and resid 302 through 316
      removed outlier: 4.148A  pdb=" N   TYR B 306 " --> pdb=" O   LYS B 302 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LEU B 311 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   VAL B 314 " --> pdb=" O   SER B 310 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE B 316 " --> pdb=" O   PHE B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 336
      removed outlier: 3.769A  pdb=" N   TYR B 321 " --> pdb=" O   PHE B 317 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   CYS B 324 " --> pdb=" O   PHE B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 473
      removed outlier: 4.201A  pdb=" N   ILE B 448 " --> pdb=" O   TYR B 444 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   PHE B 454 " --> pdb=" O   THR B 450 " (cutoff:3.500A)
      Proline residue:  B 458  - end of helix
      removed outlier: 3.750A  pdb=" N   GLN B 461 " --> pdb=" O   LEU B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 501
    Processing helix  chain 'B' and resid 502 through 524
      removed outlier: 3.576A  pdb=" N   LEU B 507 " --> pdb=" O   GLY B 503 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU B 510 " --> pdb=" O   LEU B 506 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   PHE B 511 " --> pdb=" O   LEU B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 561
      removed outlier: 4.202A  pdb=" N   LEU B 552 " --> pdb=" O   MET B 548 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLY B 556 " --> pdb=" O   LEU B 552 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 577
    Processing helix  chain 'B' and resid 577 through 591
    Processing helix  chain 'B' and resid 609 through 619
      removed outlier: 3.787A  pdb=" N   THR B 615 " --> pdb=" O   VAL B 611 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   VAL B 616 " --> pdb=" O   ILE B 612 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   VAL B 619 " --> pdb=" O   THR B 615 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 644
      removed outlier: 3.554A  pdb=" N   ALA B 634 " --> pdb=" O   VAL B 630 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL B 637 " --> pdb=" O   SER B 633 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 686 through 705
      removed outlier: 3.525A  pdb=" N   VAL B 698 " --> pdb=" O   VAL B 694 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   ASN B 699 " --> pdb=" O   GLY B 695 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU B 704 " --> pdb=" O   TRP B 700 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 706 through 708
      No H-bonds generated for 'chain 'B' and resid 706 through 708'
    Processing helix  chain 'B' and resid 716 through 740
      removed outlier: 3.808A  pdb=" N   PHE B 722 " --> pdb=" O   MET B 718 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE B 723 " --> pdb=" O   LEU B 719 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   CYS B 724 " --> pdb=" O   GLY B 720 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU B 728 " --> pdb=" O   CYS B 724 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   SER B 740 " --> pdb=" O   MET B 736 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 745 through 767
      removed outlier: 3.863A  pdb=" N   LEU B 749 " --> pdb=" O   LEU B 745 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   CYS B 751 " --> pdb=" O   VAL B 747 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA B 756 " --> pdb=" O   ILE B 752 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   VAL B 757 " --> pdb=" O   VAL B 753 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   MET B 758 " --> pdb=" O   ALA B 754 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   TYR B 764 " --> pdb=" O   ALA B 760 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   PHE B 765 " --> pdb=" O   ALA B 761 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   PHE B 767 " --> pdb=" O   LEU B 763 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 778 through 782
    Processing helix  chain 'B' and resid 796 through 817
      removed outlier: 3.585A  pdb=" N   HIS B 800 " --> pdb=" O   HIS B 796 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU B 802 " --> pdb=" O   ILE B 798 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA B 804 " --> pdb=" O   HIS B 800 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ALA B 806 " --> pdb=" O   LEU B 802 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU B 812 " --> pdb=" O   PHE B 808 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   VAL B 813 " --> pdb=" O   PHE B 809 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU B 814 " --> pdb=" O   SER B 810 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 818 through 825
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56
      removed outlier: 3.610A  pdb=" N   GLY A  54 " --> pdb=" O   TYR A 159 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR A 159 " --> pdb=" O   GLY A  54 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL A  56 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LYS A 160 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR A 164 " --> pdb=" O   ARG A  79 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ARG A  79 " --> pdb=" O   THR A 164 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   VAL A 125 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 66
    Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 181
      removed outlier: 3.600A  pdb=" N   PHE A 179 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LYS A 291 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 187 through 192
      removed outlier: 3.653A  pdb=" N   VAL A 236 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 56
      removed outlier: 3.611A  pdb=" N   GLY B  54 " --> pdb=" O   TYR B 159 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR B 159 " --> pdb=" O   GLY B  54 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL B  56 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LYS B 160 " --> pdb=" O   ASN B  83 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR B 164 " --> pdb=" O   ARG B  79 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ARG B  79 " --> pdb=" O   THR B 164 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   VAL B 125 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 62 through 66
    Processing sheet with id=AA7, first strand: chain 'B' and resid 179 through 181
      removed outlier: 3.602A  pdb=" N   PHE B 179 " --> pdb=" O   LEU B 293 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LYS B 291 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.654A  pdb=" N   VAL B 236 " --> pdb=" O   VAL B 217 " (cutoff:3.500A)

    421 hydrogen bonds defined for protein.
    1209 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: 1.38

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3033
        1.34 -     1.46: 2682
        1.46 -     1.58: 4583
        1.58 -     1.70: 0
        1.70 -     1.82: 94
  Bond restraints: 10392
  Sorted by residual:
  bond pdb=" CA  PHE B 809 "
       pdb=" C   PHE B 809 "
    ideal  model  delta    sigma   weight residual
    1.524  1.433  0.091 1.48e-02 4.57e+03 3.80e+01
  bond pdb=" CA  PHE A 809 "
       pdb=" C   PHE A 809 "
    ideal  model  delta    sigma   weight residual
    1.524  1.434  0.091 1.48e-02 4.57e+03 3.74e+01
  bond pdb=" CA  SER B 780 "
       pdb=" C   SER B 780 "
    ideal  model  delta    sigma   weight residual
    1.523  1.471  0.052 1.80e-02 3.09e+03 8.34e+00
  bond pdb=" CA  SER A 780 "
       pdb=" C   SER A 780 "
    ideal  model  delta    sigma   weight residual
    1.523  1.471  0.052 1.80e-02 3.09e+03 8.30e+00
  bond pdb=" CB  VAL A 463 "
       pdb=" CG1 VAL A 463 "
    ideal  model  delta    sigma   weight residual
    1.521  1.435  0.086 3.30e-02 9.18e+02 6.77e+00
  ... (remaining 10387 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.93: 13655
        2.93 -     5.86: 396
        5.86 -     8.79: 66
        8.79 -    11.72: 9
       11.72 -    14.65: 2
  Bond angle restraints: 14128
  Sorted by residual:
  angle pdb=" C   PHE A  48 "
        pdb=" N   ASP A  49 "
        pdb=" CA  ASP A  49 "
      ideal   model   delta    sigma   weight residual
     121.54  131.81  -10.27 1.91e+00 2.74e-01 2.89e+01
  angle pdb=" C   PHE B  48 "
        pdb=" N   ASP B  49 "
        pdb=" CA  ASP B  49 "
      ideal   model   delta    sigma   weight residual
     121.54  131.77  -10.23 1.91e+00 2.74e-01 2.87e+01
  angle pdb=" N   GLN B  99 "
        pdb=" CA  GLN B  99 "
        pdb=" C   GLN B  99 "
      ideal   model   delta    sigma   weight residual
     111.34  118.64   -7.30 1.49e+00 4.50e-01 2.40e+01
  angle pdb=" N   GLN A  99 "
        pdb=" CA  GLN A  99 "
        pdb=" C   GLN A  99 "
      ideal   model   delta    sigma   weight residual
     111.34  118.61   -7.27 1.49e+00 4.50e-01 2.38e+01
  angle pdb=" C   GLN B 646 "
        pdb=" N   ILE B 647 "
        pdb=" CA  ILE B 647 "
      ideal   model   delta    sigma   weight residual
     121.97  130.25   -8.28 1.80e+00 3.09e-01 2.12e+01
  ... (remaining 14123 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.41: 5628
       16.41 -    32.82: 326
       32.82 -    49.23: 76
       49.23 -    65.64: 2
       65.64 -    82.05: 16
  Dihedral angle restraints: 6048
    sinusoidal: 2348
      harmonic: 3700
  Sorted by residual:
  dihedral pdb=" CA  VAL B 108 "
           pdb=" C   VAL B 108 "
           pdb=" N   PRO B 109 "
           pdb=" CA  PRO B 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -109.03  -70.97     0      5.00e+00 4.00e-02 2.01e+02
  dihedral pdb=" CA  VAL A 108 "
           pdb=" C   VAL A 108 "
           pdb=" N   PRO A 109 "
           pdb=" CA  PRO A 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -109.09  -70.91     0      5.00e+00 4.00e-02 2.01e+02
  dihedral pdb=" CA  TYR A 210 "
           pdb=" C   TYR A 210 "
           pdb=" N   PRO A 211 "
           pdb=" CA  PRO A 211 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  121.55   58.45     0      5.00e+00 4.00e-02 1.37e+02
  ... (remaining 6045 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1235
       0.076 -    0.152: 306
       0.152 -    0.227: 53
       0.227 -    0.303: 8
       0.303 -    0.379: 4
  Chirality restraints: 1606
  Sorted by residual:
  chirality pdb=" CB  ILE B 220 "
            pdb=" CA  ILE B 220 "
            pdb=" CG1 ILE B 220 "
            pdb=" CG2 ILE B 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.38 2.00e-01 2.50e+01 3.59e+00
  chirality pdb=" CB  ILE A 220 "
            pdb=" CA  ILE A 220 "
            pdb=" CG1 ILE A 220 "
            pdb=" CG2 ILE A 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.38 2.00e-01 2.50e+01 3.53e+00
  chirality pdb=" CB  ILE A 538 "
            pdb=" CA  ILE A 538 "
            pdb=" CG1 ILE A 538 "
            pdb=" CG2 ILE A 538 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.34 2.00e-01 2.50e+01 2.83e+00
  ... (remaining 1603 not shown)

  Planarity restraints: 1750
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 210 "    0.066 5.00e-02 4.00e+02   9.85e-02 1.55e+01
        pdb=" N   PRO B 211 "   -0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO B 211 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B 211 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 210 "   -0.066 5.00e-02 4.00e+02   9.85e-02 1.55e+01
        pdb=" N   PRO A 211 "    0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO A 211 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 211 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 108 "    0.064 5.00e-02 4.00e+02   9.65e-02 1.49e+01
        pdb=" N   PRO B 109 "   -0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO B 109 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B 109 "    0.052 5.00e-02 4.00e+02
  ... (remaining 1747 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 2869
        2.79 -     3.32: 9140
        3.32 -     3.85: 15184
        3.85 -     4.37: 16961
        4.37 -     4.90: 29141
  Nonbonded interactions: 73295
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 124 "
            pdb=" OG  SER A 184 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   GLU B 124 "
            pdb=" OG  SER B 184 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   CYS A 751 "
            pdb=" OG1 THR A 755 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   CYS B 751 "
            pdb=" OG1 THR B 755 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   PRO A 266 "
            pdb=" NH1 ARG A 289 "
     model   vdw
     2.307 3.120
  ... (remaining 73290 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.520
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.810
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
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      :  0.012   0.095  10398  Z= 0.501
  Angle     :  1.247  14.651  14140  Z= 0.677
  Chirality :  0.071   0.379   1606
  Planarity :  0.009   0.099   1750
  Dihedral  : 11.902  82.050   3642
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  : 10.75 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  4.29 %
    Favored  : 95.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 13.64 %
    Twisted General : 0.34 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.36 (0.17), residues: 1228
  helix: -4.01 (0.12), residues: 468
  sheet: -1.84 (0.32), residues: 242
  loop : -3.88 (0.21), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A  79 
 TYR   0.026   0.004   TYR A 481 
 PHE   0.032   0.004   PHE B 509 
 TRP   0.021   0.003   TRP A 799 
 HIS   0.007   0.002   HIS B 800 

Details of bonding type rmsd
  covalent geometry    : bond        0.01155 (10392)
  covalent geometry    : angle       1.24481 (14128)
  SS BOND              : bond        0.01715 (    6)
  SS BOND              : angle       2.57423 (   12)
  hydrogen bonds       : bond        0.31230 (  421)
  hydrogen bonds       : angle       9.79948 ( 1209)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 244
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.7557 (t80) cc_final: 0.7151 (t80)
REVERT: A  101 LYS cc_start: 0.8654 (mttt) cc_final: 0.7945 (mtpp)
REVERT: A  232 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7756 (mt-10)
REVERT: A  689 MET cc_start: 0.6895 (ttm) cc_final: 0.6557 (ttm)
REVERT: A  699 ASN cc_start: 0.9005 (p0) cc_final: 0.8598 (p0)
REVERT: A  719 LEU cc_start: 0.8780 (mm) cc_final: 0.8539 (mt)
REVERT: B   81 TYR cc_start: 0.7340 (t80) cc_final: 0.7110 (t80)
REVERT: B  101 LYS cc_start: 0.8646 (mttt) cc_final: 0.7934 (mtpp)
REVERT: B  168 HIS cc_start: 0.6601 (p90) cc_final: 0.6400 (p90)
REVERT: B  232 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7763 (mt-10)
REVERT: B  689 MET cc_start: 0.7004 (ttm) cc_final: 0.6662 (ttm)
REVERT: B  699 ASN cc_start: 0.9015 (p0) cc_final: 0.8622 (p0)
REVERT: B  719 LEU cc_start: 0.8788 (mm) cc_final: 0.8547 (mt)
  outliers start: 4
  outliers final: 2
  residues processed: 248
  average time/residue: 0.0803
  time to fit residues: 29.1102
Evaluate side-chains
  155 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 153
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain B residue  261 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0970
   chunk 123 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
A 475 ASN
B  83 ASN
B 475 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.166675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.125223 restraints weight = 17028.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.124826 restraints weight = 11324.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.126351 restraints weight = 9275.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.127036 restraints weight = 7831.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.126875 restraints weight = 7206.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10398  Z= 0.144
  Angle     :  0.717   8.772  14140  Z= 0.377
  Chirality :  0.047   0.185   1606
  Planarity :  0.006   0.078   1750
  Dihedral  :  6.960  60.992   1356
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.41 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 10.64 %
    Favored  : 87.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 18.18 %
    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: -3.72 (0.20), residues: 1228
  helix: -1.91 (0.18), residues: 498
  sheet: -1.43 (0.31), residues: 266
  loop : -3.63 (0.24), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 710 
 TYR   0.018   0.001   TYR B 481 
 PHE   0.030   0.002   PHE B 705 
 TRP   0.009   0.001   TRP B 700 
 HIS   0.004   0.001   HIS A 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (10392)
  covalent geometry    : angle       0.71642 (14128)
  SS BOND              : bond        0.00312 (    6)
  SS BOND              : angle       1.21584 (   12)
  hydrogen bonds       : bond        0.05235 (  421)
  hydrogen bonds       : angle       5.72283 ( 1209)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 186
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.7170 (t80) cc_final: 0.6951 (t80)
REVERT: A  232 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7005 (pt0)
REVERT: A  484 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8426 (tt)
REVERT: A  578 MET cc_start: 0.8770 (tpp) cc_final: 0.8346 (mmm)
REVERT: A  613 MET cc_start: 0.8066 (mmp) cc_final: 0.7402 (ppp)
REVERT: A  689 MET cc_start: 0.6724 (ttm) cc_final: 0.6360 (ttp)
REVERT: A  699 ASN cc_start: 0.8818 (p0) cc_final: 0.8557 (p0)
REVERT: B   81 TYR cc_start: 0.7177 (t80) cc_final: 0.6930 (t80)
REVERT: B  155 LEU cc_start: 0.8065 (mp) cc_final: 0.7730 (tt)
REVERT: B  232 GLU cc_start: 0.7756 (mt-10) cc_final: 0.6997 (pt0)
REVERT: B  484 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8381 (tt)
REVERT: B  578 MET cc_start: 0.8780 (tpp) cc_final: 0.8362 (mmm)
REVERT: B  613 MET cc_start: 0.8054 (mmp) cc_final: 0.7387 (ppp)
REVERT: B  689 MET cc_start: 0.6830 (ttm) cc_final: 0.6461 (ttp)
REVERT: B  699 ASN cc_start: 0.8817 (p0) cc_final: 0.8564 (p0)
  outliers start: 20
  outliers final: 7
  residues processed: 201
  average time/residue: 0.0768
  time to fit residues: 22.7178
Evaluate side-chains
  152 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 143
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  787 CYS
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  787 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0070
   chunk 22 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 123 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0570
   chunk 61 optimal weight:    5.9990
   chunk 83 optimal weight:    0.5980
   overall best weight:    0.9320

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
A 168 HIS
B  62 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.166293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.123872 restraints weight = 16893.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.124192 restraints weight = 11192.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.124963 restraints weight = 8500.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.125608 restraints weight = 7961.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.125792 restraints weight = 7143.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10398  Z= 0.141
  Angle     :  0.674   8.057  14140  Z= 0.352
  Chirality :  0.046   0.208   1606
  Planarity :  0.006   0.080   1750
  Dihedral  :  6.470  58.555   1356
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.06 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.42 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.22), residues: 1228
  helix: -0.66 (0.21), residues: 500
  sheet: -1.00 (0.32), residues: 266
  loop : -3.49 (0.25), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 710 
 TYR   0.014   0.001   TYR B 481 
 PHE   0.020   0.002   PHE B 705 
 TRP   0.013   0.001   TRP A 106 
 HIS   0.005   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (10392)
  covalent geometry    : angle       0.67383 (14128)
  SS BOND              : bond        0.00259 (    6)
  SS BOND              : angle       1.00328 (   12)
  hydrogen bonds       : bond        0.04405 (  421)
  hydrogen bonds       : angle       5.08343 ( 1209)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 165
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A   81 TYR cc_start: 0.7094 (t80) cc_final: 0.6845 (t80)
REVERT: A  232 GLU cc_start: 0.7741 (mt-10) cc_final: 0.6908 (pt0)
REVERT: A  578 MET cc_start: 0.8660 (tpp) cc_final: 0.8236 (mmm)
REVERT: A  613 MET cc_start: 0.8025 (mmp) cc_final: 0.7440 (ppp)
REVERT: A  689 MET cc_start: 0.7148 (ttm) cc_final: 0.6768 (ttp)
REVERT: A  699 ASN cc_start: 0.8842 (p0) cc_final: 0.8596 (p0)
REVERT: A  718 MET cc_start: 0.8550 (mmm) cc_final: 0.8331 (mmm)
REVERT: B   81 TYR cc_start: 0.7198 (t80) cc_final: 0.6725 (t80)
REVERT: B  155 LEU cc_start: 0.8106 (mp) cc_final: 0.7819 (tt)
REVERT: B  232 GLU cc_start: 0.7741 (mt-10) cc_final: 0.6915 (pt0)
REVERT: B  578 MET cc_start: 0.8657 (tpp) cc_final: 0.8246 (mmm)
REVERT: B  613 MET cc_start: 0.8023 (mmp) cc_final: 0.7446 (ppp)
REVERT: B  699 ASN cc_start: 0.8860 (p0) cc_final: 0.8635 (p0)
REVERT: B  718 MET cc_start: 0.8552 (mmm) cc_final: 0.8341 (mmm)
  outliers start: 26
  outliers final: 11
  residues processed: 186
  average time/residue: 0.0654
  time to fit residues: 19.2461
Evaluate side-chains
  156 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  787 CYS
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  787 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 106 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 37 optimal weight:   50.0000
   chunk 42 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0170
   chunk 75 optimal weight:    0.0170
   chunk 123 optimal weight:    4.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.4856

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

Flipped N/Q/H residues before XYZ refinement:
A 168 HIS
A 238 GLN
B 168 HIS
B 238 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.169480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.127716 restraints weight = 17027.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.128231 restraints weight = 10949.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.128985 restraints weight = 9488.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.129576 restraints weight = 7742.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.129753 restraints weight = 6901.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.4033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10398  Z= 0.119
  Angle     :  0.666  10.229  14140  Z= 0.338
  Chirality :  0.046   0.319   1606
  Planarity :  0.005   0.089   1750
  Dihedral  :  6.161  58.365   1356
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.68 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.38 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -1.96 (0.23), residues: 1228
  helix: -0.02 (0.22), residues: 508
  sheet: -0.11 (0.34), residues: 236
  loop : -3.42 (0.24), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 710 
 TYR   0.014   0.001   TYR B 481 
 PHE   0.020   0.001   PHE A 169 
 TRP   0.014   0.001   TRP A 106 
 HIS   0.015   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (10392)
  covalent geometry    : angle       0.66648 (14128)
  SS BOND              : bond        0.00514 (    6)
  SS BOND              : angle       0.68342 (   12)
  hydrogen bonds       : bond        0.03692 (  421)
  hydrogen bonds       : angle       4.61248 ( 1209)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 165
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A   81 TYR cc_start: 0.6815 (t80) cc_final: 0.6391 (t80)
REVERT: A  232 GLU cc_start: 0.7723 (mt-10) cc_final: 0.6863 (pt0)
REVERT: A  484 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8650 (tt)
REVERT: A  507 LEU cc_start: 0.9023 (tp) cc_final: 0.8673 (tp)
REVERT: A  578 MET cc_start: 0.8595 (tpp) cc_final: 0.8216 (mmm)
REVERT: A  580 MET cc_start: 0.8670 (ttm) cc_final: 0.8435 (ttm)
REVERT: A  613 MET cc_start: 0.7993 (mmp) cc_final: 0.7452 (ptt)
REVERT: A  686 MET cc_start: 0.7123 (pmm) cc_final: 0.6235 (pmm)
REVERT: A  689 MET cc_start: 0.7173 (ttm) cc_final: 0.6804 (ptm)
REVERT: B   81 TYR cc_start: 0.7191 (t80) cc_final: 0.6833 (t80)
REVERT: B  155 LEU cc_start: 0.8039 (mp) cc_final: 0.7775 (tt)
REVERT: B  232 GLU cc_start: 0.7727 (mt-10) cc_final: 0.6884 (pt0)
REVERT: B  555 GLU cc_start: 0.8280 (tp30) cc_final: 0.8002 (tp30)
REVERT: B  578 MET cc_start: 0.8594 (tpp) cc_final: 0.8189 (mmm)
REVERT: B  580 MET cc_start: 0.8642 (ttm) cc_final: 0.8359 (ttm)
REVERT: B  613 MET cc_start: 0.7991 (mmp) cc_final: 0.7457 (ptt)
  outliers start: 28
  outliers final: 19
  residues processed: 183
  average time/residue: 0.0637
  time to fit residues: 18.5644
Evaluate side-chains
  170 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 150
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  797 ASP
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  212 CYS
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  797 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 90 optimal weight:    8.9990
   chunk 43 optimal weight:    6.9990
   chunk 20 optimal weight:    0.0670
   chunk 4 optimal weight:    0.4980
   chunk 18 optimal weight:    4.9990
   chunk 121 optimal weight:    4.9990
   chunk 118 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0870
   overall best weight:    0.4096

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

Flipped N/Q/H residues before XYZ refinement:
A 168 HIS
A 238 GLN
A 699 ASN
B 168 HIS
B 238 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.170564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.128704 restraints weight = 16842.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.128820 restraints weight = 11271.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.130031 restraints weight = 9481.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.130898 restraints weight = 7615.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.130832 restraints weight = 6829.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.4317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10398  Z= 0.112
  Angle     :  0.636   7.633  14140  Z= 0.324
  Chirality :  0.045   0.269   1606
  Planarity :  0.005   0.089   1750
  Dihedral  :  5.973  58.110   1356
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.68 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.46 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -1.54 (0.24), residues: 1228
  helix:  0.34 (0.23), residues: 516
  sheet:  0.07 (0.34), residues: 238
  loop : -3.26 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 710 
 TYR   0.014   0.001   TYR B  81 
 PHE   0.019   0.001   PHE B 702 
 TRP   0.011   0.001   TRP B 106 
 HIS   0.008   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (10392)
  covalent geometry    : angle       0.63649 (14128)
  SS BOND              : bond        0.00242 (    6)
  SS BOND              : angle       0.54339 (   12)
  hydrogen bonds       : bond        0.03420 (  421)
  hydrogen bonds       : angle       4.40762 ( 1209)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A  232 GLU cc_start: 0.7698 (mt-10) cc_final: 0.6833 (pt0)
REVERT: A  578 MET cc_start: 0.8611 (tpp) cc_final: 0.8150 (mmm)
REVERT: A  580 MET cc_start: 0.8659 (ttm) cc_final: 0.8376 (ttm)
REVERT: A  613 MET cc_start: 0.7995 (mmp) cc_final: 0.7462 (ptt)
REVERT: A  686 MET cc_start: 0.7065 (pmm) cc_final: 0.6213 (pmm)
REVERT: A  689 MET cc_start: 0.7218 (ttm) cc_final: 0.6862 (ptm)
REVERT: B  232 GLU cc_start: 0.7682 (mt-10) cc_final: 0.6817 (pt0)
REVERT: B  578 MET cc_start: 0.8602 (tpp) cc_final: 0.8164 (mmm)
REVERT: B  580 MET cc_start: 0.8610 (ttm) cc_final: 0.8373 (ttm)
REVERT: B  613 MET cc_start: 0.7994 (mmp) cc_final: 0.7447 (ptt)
  outliers start: 29
  outliers final: 19
  residues processed: 170
  average time/residue: 0.0687
  time to fit residues: 18.3409
Evaluate side-chains
  152 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  585 CYS
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  797 ASP
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  757 VAL
Chi-restraints excluded: chain B residue  797 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   chunk 105 optimal weight:    9.9990
   chunk 92 optimal weight:    0.0030
   chunk 42 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 110 optimal weight:   20.0000
   chunk 76 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 111 optimal weight:    5.9990
   overall best weight:    2.1596

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

Flipped N/Q/H residues before XYZ refinement:
A 168 HIS
B 168 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.162371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.118871 restraints weight = 17160.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.119659 restraints weight = 11358.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.120864 restraints weight = 8726.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.121208 restraints weight = 7361.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.121245 restraints weight = 6755.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.4210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10398  Z= 0.218
  Angle     :  0.720   8.338  14140  Z= 0.374
  Chirality :  0.049   0.234   1606
  Planarity :  0.006   0.099   1750
  Dihedral  :  6.377  62.555   1356
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.79 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.44 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -1.51 (0.24), residues: 1228
  helix:  0.51 (0.23), residues: 516
  sheet:  0.01 (0.34), residues: 236
  loop : -3.37 (0.25), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 172 
 TYR   0.023   0.002   TYR B 188 
 PHE   0.027   0.002   PHE B 509 
 TRP   0.013   0.001   TRP A 106 
 HIS   0.016   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 (10392)
  covalent geometry    : angle       0.71983 (14128)
  SS BOND              : bond        0.00421 (    6)
  SS BOND              : angle       0.94527 (   12)
  hydrogen bonds       : bond        0.04555 (  421)
  hydrogen bonds       : angle       4.86170 ( 1209)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 139
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A   81 TYR cc_start: 0.7016 (t80) cc_final: 0.6541 (t80)
REVERT: A  232 GLU cc_start: 0.7714 (mt-10) cc_final: 0.6851 (pt0)
REVERT: A  578 MET cc_start: 0.8581 (tpp) cc_final: 0.8259 (mmm)
REVERT: B   81 TYR cc_start: 0.7097 (t80) cc_final: 0.6726 (t80)
REVERT: B  232 GLU cc_start: 0.7706 (mt-10) cc_final: 0.6853 (pt0)
REVERT: B  578 MET cc_start: 0.8614 (tpp) cc_final: 0.8248 (mmm)
  outliers start: 39
  outliers final: 24
  residues processed: 169
  average time/residue: 0.0673
  time to fit residues: 17.6983
Evaluate side-chains
  159 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  585 CYS
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  787 CYS
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  485 CYS
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  509 PHE
Chi-restraints excluded: chain B residue  721 ILE
Chi-restraints excluded: chain B residue  757 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 114 optimal weight:    0.0470
   chunk 25 optimal weight:    0.8980
   chunk 4 optimal weight:    0.2980
   chunk 56 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.6480

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

Flipped N/Q/H residues before XYZ refinement:
A 238 GLN
B 238 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.157462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.116973 restraints weight = 16445.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.116834 restraints weight = 10338.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.118081 restraints weight = 7803.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.119306 restraints weight = 6461.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.119460 restraints weight = 5682.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.4604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10398  Z= 0.123
  Angle     :  0.645   7.957  14140  Z= 0.331
  Chirality :  0.045   0.235   1606
  Planarity :  0.005   0.093   1750
  Dihedral  :  6.092  59.322   1356
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.57 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.98 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -1.30 (0.24), residues: 1228
  helix:  0.60 (0.23), residues: 532
  sheet:  0.19 (0.34), residues: 236
  loop : -3.32 (0.25), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 523 
 TYR   0.018   0.001   TYR A  81 
 PHE   0.029   0.001   PHE A 750 
 TRP   0.011   0.001   TRP A 700 
 HIS   0.009   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (10392)
  covalent geometry    : angle       0.64501 (14128)
  SS BOND              : bond        0.00242 (    6)
  SS BOND              : angle       0.62282 (   12)
  hydrogen bonds       : bond        0.03560 (  421)
  hydrogen bonds       : angle       4.44835 ( 1209)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 141
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A  232 GLU cc_start: 0.7812 (mt-10) cc_final: 0.6886 (pt0)
REVERT: A  475 ASN cc_start: 0.8611 (t0) cc_final: 0.8339 (t0)
REVERT: A  578 MET cc_start: 0.8627 (tpp) cc_final: 0.8257 (mmm)
REVERT: A  613 MET cc_start: 0.7720 (mmp) cc_final: 0.7190 (ppp)
REVERT: B   81 TYR cc_start: 0.7109 (t80) cc_final: 0.6666 (t80)
REVERT: B  232 GLU cc_start: 0.7809 (mt-10) cc_final: 0.6891 (pt0)
REVERT: B  475 ASN cc_start: 0.8618 (t0) cc_final: 0.8348 (t0)
REVERT: B  578 MET cc_start: 0.8625 (tpp) cc_final: 0.8232 (mmm)
REVERT: B  613 MET cc_start: 0.7727 (mmp) cc_final: 0.7219 (ppp)
  outliers start: 32
  outliers final: 23
  residues processed: 166
  average time/residue: 0.0673
  time to fit residues: 17.1729
Evaluate side-chains
  157 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  585 CYS
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  797 ASP
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  509 PHE
Chi-restraints excluded: chain B residue  721 ILE
Chi-restraints excluded: chain B residue  757 VAL
Chi-restraints excluded: chain B residue  797 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 123 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 168 HIS
A 238 GLN
B 238 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.156252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.113651 restraints weight = 16907.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.114599 restraints weight = 10530.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.115997 restraints weight = 7615.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.116205 restraints weight = 6520.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.116285 restraints weight = 6092.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.4668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10398  Z= 0.156
  Angle     :  0.662   8.395  14140  Z= 0.341
  Chirality :  0.046   0.226   1606
  Planarity :  0.006   0.096   1750
  Dihedral  :  6.110  59.699   1356
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.55 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 17.89 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -1.16 (0.24), residues: 1228
  helix:  0.76 (0.23), residues: 528
  sheet:  0.30 (0.34), residues: 236
  loop : -3.29 (0.25), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 524 
 TYR   0.018   0.001   TYR B 188 
 PHE   0.029   0.002   PHE A 750 
 TRP   0.010   0.001   TRP A 106 
 HIS   0.005   0.001   HIS B 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (10392)
  covalent geometry    : angle       0.66179 (14128)
  SS BOND              : bond        0.00354 (    6)
  SS BOND              : angle       0.74176 (   12)
  hydrogen bonds       : bond        0.03891 (  421)
  hydrogen bonds       : angle       4.50606 ( 1209)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 142
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A  232 GLU cc_start: 0.7788 (mt-10) cc_final: 0.6894 (pt0)
REVERT: A  578 MET cc_start: 0.8628 (tpp) cc_final: 0.8298 (mmm)
REVERT: A  613 MET cc_start: 0.8005 (mmp) cc_final: 0.7309 (ppp)
REVERT: B   81 TYR cc_start: 0.7180 (t80) cc_final: 0.6810 (t80)
REVERT: B  232 GLU cc_start: 0.7787 (mt-10) cc_final: 0.6900 (pt0)
REVERT: B  578 MET cc_start: 0.8636 (tpp) cc_final: 0.8280 (mmm)
REVERT: B  613 MET cc_start: 0.8000 (mmp) cc_final: 0.7329 (ppp)
REVERT: B  689 MET cc_start: 0.7611 (ttp) cc_final: 0.7375 (ptp)
  outliers start: 35
  outliers final: 28
  residues processed: 168
  average time/residue: 0.0759
  time to fit residues: 19.2191
Evaluate side-chains
  161 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  509 PHE
Chi-restraints excluded: chain A residue  585 CYS
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  797 ASP
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  485 CYS
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  509 PHE
Chi-restraints excluded: chain B residue  721 ILE
Chi-restraints excluded: chain B residue  757 VAL
Chi-restraints excluded: chain B residue  787 CYS
Chi-restraints excluded: chain B residue  797 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 110 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 30 optimal weight:    0.7980
   chunk 99 optimal weight:    0.0470
   chunk 117 optimal weight:    0.9980
   chunk 113 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 108 optimal weight:    5.9990
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
A 238 GLN
B 238 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.158194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.117782 restraints weight = 16440.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.117286 restraints weight = 10847.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.118523 restraints weight = 8092.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.120233 restraints weight = 6761.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.120377 restraints weight = 5733.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.4911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10398  Z= 0.121
  Angle     :  0.645   8.228  14140  Z= 0.330
  Chirality :  0.046   0.240   1606
  Planarity :  0.005   0.092   1750
  Dihedral  :  5.944  56.793   1356
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 20.04 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -0.99 (0.24), residues: 1228
  helix:  0.79 (0.23), residues: 528
  sheet:  0.04 (0.33), residues: 258
  loop : -2.97 (0.26), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 524 
 TYR   0.018   0.001   TYR A  81 
 PHE   0.033   0.001   PHE A 750 
 TRP   0.011   0.001   TRP B 700 
 HIS   0.007   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (10392)
  covalent geometry    : angle       0.64507 (14128)
  SS BOND              : bond        0.00197 (    6)
  SS BOND              : angle       0.61574 (   12)
  hydrogen bonds       : bond        0.03407 (  421)
  hydrogen bonds       : angle       4.29565 ( 1209)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A  232 GLU cc_start: 0.7749 (mt-10) cc_final: 0.6825 (pt0)
REVERT: A  578 MET cc_start: 0.8631 (tpp) cc_final: 0.8257 (mmm)
REVERT: A  613 MET cc_start: 0.7947 (mmp) cc_final: 0.7332 (ppp)
REVERT: B   81 TYR cc_start: 0.7156 (t80) cc_final: 0.6720 (t80)
REVERT: B  232 GLU cc_start: 0.7766 (mt-10) cc_final: 0.6851 (pt0)
REVERT: B  578 MET cc_start: 0.8622 (tpp) cc_final: 0.8222 (mmm)
REVERT: B  613 MET cc_start: 0.7947 (mmp) cc_final: 0.7321 (ppp)
REVERT: B  689 MET cc_start: 0.7620 (ttp) cc_final: 0.7385 (ptp)
  outliers start: 22
  outliers final: 21
  residues processed: 160
  average time/residue: 0.0764
  time to fit residues: 18.6643
Evaluate side-chains
  156 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  509 PHE
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  787 CYS
Chi-restraints excluded: chain A residue  797 ASP
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  721 ILE
Chi-restraints excluded: chain B residue  757 VAL
Chi-restraints excluded: chain B residue  787 CYS
Chi-restraints excluded: chain B residue  797 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 108 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0060
   chunk 95 optimal weight:    0.0670
   chunk 21 optimal weight:    0.8980
   chunk 50 optimal weight:   10.0000
   chunk 121 optimal weight:    3.9990
   chunk 98 optimal weight:    9.9990
   chunk 94 optimal weight:    0.9980
   overall best weight:    0.9936

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

Flipped N/Q/H residues before XYZ refinement:
A 168 HIS
A 238 GLN
B 238 GLN
B 475 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.157326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.115198 restraints weight = 16204.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.118192 restraints weight = 9399.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.119773 restraints weight = 6282.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.119397 restraints weight = 5605.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.119515 restraints weight = 5395.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.4962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10398  Z= 0.135
  Angle     :  0.656   8.000  14140  Z= 0.336
  Chirality :  0.046   0.235   1606
  Planarity :  0.005   0.094   1750
  Dihedral  :  5.928  57.213   1356
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 20.13 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -0.94 (0.24), residues: 1228
  helix:  0.81 (0.23), residues: 528
  sheet:  0.08 (0.33), residues: 258
  loop : -2.93 (0.26), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 524 
 TYR   0.018   0.001   TYR A  81 
 PHE   0.034   0.002   PHE A 750 
 TRP   0.012   0.001   TRP B 700 
 HIS   0.005   0.001   HIS B 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (10392)
  covalent geometry    : angle       0.65645 (14128)
  SS BOND              : bond        0.00170 (    6)
  SS BOND              : angle       0.64954 (   12)
  hydrogen bonds       : bond        0.03593 (  421)
  hydrogen bonds       : angle       4.33655 ( 1209)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 139
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A  232 GLU cc_start: 0.7767 (mt-10) cc_final: 0.6872 (pt0)
REVERT: A  475 ASN cc_start: 0.8628 (t0) cc_final: 0.8375 (t0)
REVERT: A  578 MET cc_start: 0.8632 (tpp) cc_final: 0.8254 (mmm)
REVERT: A  613 MET cc_start: 0.8009 (mmp) cc_final: 0.7358 (ppp)
REVERT: A  798 ILE cc_start: 0.9065 (pt) cc_final: 0.8665 (mm)
REVERT: B   81 TYR cc_start: 0.7264 (t80) cc_final: 0.6842 (t80)
REVERT: B  232 GLU cc_start: 0.7849 (mt-10) cc_final: 0.6904 (pt0)
REVERT: B  578 MET cc_start: 0.8653 (tpp) cc_final: 0.8253 (mmm)
REVERT: B  613 MET cc_start: 0.8012 (mmp) cc_final: 0.7355 (ppp)
REVERT: B  798 ILE cc_start: 0.9049 (pt) cc_final: 0.8646 (mm)
  outliers start: 25
  outliers final: 23
  residues processed: 157
  average time/residue: 0.0677
  time to fit residues: 16.5846
Evaluate side-chains
  158 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  485 CYS
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  509 PHE
Chi-restraints excluded: chain A residue  585 CYS
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  787 CYS
Chi-restraints excluded: chain A residue  797 ASP
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  721 ILE
Chi-restraints excluded: chain B residue  757 VAL
Chi-restraints excluded: chain B residue  787 CYS
Chi-restraints excluded: chain B residue  797 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 83 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 113 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 168 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.155959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.112982 restraints weight = 17088.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.112879 restraints weight = 11300.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.114100 restraints weight = 8686.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.114792 restraints weight = 7239.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.114991 restraints weight = 6590.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.4910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10398  Z= 0.190
  Angle     :  0.690   7.884  14140  Z= 0.358
  Chirality :  0.048   0.219   1606
  Planarity :  0.006   0.098   1750
  Dihedral  :  6.151  60.342   1356
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.71 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 20.39 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -1.05 (0.24), residues: 1228
  helix:  0.78 (0.23), residues: 526
  sheet:  0.45 (0.34), residues: 234
  loop : -3.17 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 524 
 TYR   0.020   0.001   TYR B 188 
 PHE   0.033   0.002   PHE A 750 
 TRP   0.013   0.001   TRP B 106 
 HIS   0.005   0.001   HIS B 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 (10392)
  covalent geometry    : angle       0.68982 (14128)
  SS BOND              : bond        0.00260 (    6)
  SS BOND              : angle       0.84223 (   12)
  hydrogen bonds       : bond        0.04093 (  421)
  hydrogen bonds       : angle       4.56283 ( 1209)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1448.75 seconds
wall clock time: 25 minutes 46.68 seconds (1546.68 seconds total)