Starting phenix.real_space_refine
on Thu May 15 16:24:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yg0_33803/05_2025/7yg0_33803_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yg0_33803/05_2025/7yg0_33803.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yg0_33803/05_2025/7yg0_33803.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yg0_33803/05_2025/7yg0_33803.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yg0_33803/05_2025/7yg0_33803_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yg0_33803/05_2025/7yg0_33803_neut.cif"
  }
  resolution = 3.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.021
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      80      5.16       5
     C    8685      2.51       5
     N    2231      2.21       5
     O    2340      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13336
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 854, 6673
          Classifications: {'peptide': 854}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 36, 'TRANS': 817}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 6663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 854, 6663
          Classifications: {'peptide': 854}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 36, 'TRANS': 817}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 19
  Time building chain proxies: 7.30, per 1000 atoms: 0.55
  Number of scatterers: 13336
  At special positions: 0
  Unit cell: (158.992, 84.726, 111.922, 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      80     16.00
     O    2340      8.00
     N    2231      7.00
     C    8685      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 416 " - pdb=" SG  CYS A 421 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 430 " - pdb=" SG  CYS A 436 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 416 " - pdb=" SG  CYS B 421 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 430 " - pdb=" SG  CYS B 436 " distance=2.04

  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: 3.05
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3140

  Finding SS restraints...
    Secondary structure from input PDB file:
      77 helices and 2 sheets defined
      63.6% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 142 through 151
    Processing helix  chain 'A' and resid 153 through 158
    Processing helix  chain 'A' and resid 158 through 194
      removed outlier: 6.787A  pdb=" N   ILE A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 9.201A  pdb=" N   VAL A 169 " --> pdb=" O   GLN A 165 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LEU A 170 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 212
    Processing helix  chain 'A' and resid 212 through 249
      removed outlier: 3.718A  pdb=" N   ALA A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA A 232 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 277
      removed outlier: 3.600A  pdb=" N   ILE A 260 " --> pdb=" O   PRO A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 306
      removed outlier: 3.548A  pdb=" N   LEU A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 316
    Processing helix  chain 'A' and resid 321 through 329
    Processing helix  chain 'A' and resid 339 through 348
      removed outlier: 3.644A  pdb=" N   ILE A 346 " --> pdb=" O   GLY A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 351
      No H-bonds generated for 'chain 'A' and resid 349 through 351'
    Processing helix  chain 'A' and resid 353 through 361
      removed outlier: 4.211A  pdb=" N   GLY A 357 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA A 358 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE A 360 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 395
      Proline residue:  A 372  - end of helix
    Processing helix  chain 'A' and resid 418 through 424
      removed outlier: 3.559A  pdb=" N   CYS A 421 " --> pdb=" O   GLY A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 434
    Processing helix  chain 'A' and resid 445 through 451
    Processing helix  chain 'A' and resid 453 through 486
      removed outlier: 3.759A  pdb=" N   ILE A 457 " --> pdb=" O   PHE A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 497
      removed outlier: 3.646A  pdb=" N   PHE A 494 " --> pdb=" O   LEU A 491 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLY A 496 " --> pdb=" O   GLY A 493 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   LYS A 497 " --> pdb=" O   PHE A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 521
    Processing helix  chain 'A' and resid 524 through 553
      Proline residue:  A 530  - end of helix
    Processing helix  chain 'A' and resid 566 through 585
      removed outlier: 3.629A  pdb=" N   THR A 585 " --> pdb=" O   MET A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 605
      removed outlier: 3.611A  pdb=" N   ALA A 589 " --> pdb=" O   THR A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 631
      removed outlier: 3.878A  pdb=" N   ALA A 624 " --> pdb=" O   SER A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 634
      No H-bonds generated for 'chain 'A' and resid 632 through 634'
    Processing helix  chain 'A' and resid 655 through 665
      removed outlier: 4.194A  pdb=" N   VAL A 659 " --> pdb=" O   ARG A 655 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   PHE A 665 " --> pdb=" O   PHE A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 703
      removed outlier: 4.686A  pdb=" N   GLN A 690 " --> pdb=" O   MET A 686 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   LEU A 691 " --> pdb=" O   PRO A 687 " (cutoff:3.500A)
      removed outlier: 4.882A  pdb=" N   ILE A 692 " --> pdb=" O   GLU A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 716 through 726
      removed outlier: 3.518A  pdb=" N   LEU A 724 " --> pdb=" O   GLY A 720 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLN A 726 " --> pdb=" O   GLN A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 767
      removed outlier: 3.987A  pdb=" N   ASP A 756 " --> pdb=" O   ALA A 752 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A 761 " --> pdb=" O   TYR A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 825
      removed outlier: 5.315A  pdb=" N   PHE A 822 " --> pdb=" O   ALA A 818 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   GLN A 823 " --> pdb=" O   THR A 819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 844
      removed outlier: 3.507A  pdb=" N   THR A 843 " --> pdb=" O   GLY A 840 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 852
    Processing helix  chain 'A' and resid 854 through 858
      removed outlier: 3.792A  pdb=" N   LYS A 858 " --> pdb=" O   ARG A 855 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 875 through 884
      removed outlier: 3.743A  pdb=" N   SER A 884 " --> pdb=" O   ILE A 880 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 896 through 901
      removed outlier: 4.274A  pdb=" N   ASN A 900 " --> pdb=" O   PRO A 897 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLN A 901 " --> pdb=" O   ASP A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 914
      removed outlier: 3.518A  pdb=" N   THR A 908 " --> pdb=" O   ARG A 904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 921 through 923
      No H-bonds generated for 'chain 'A' and resid 921 through 923'
    Processing helix  chain 'A' and resid 924 through 934
    Processing helix  chain 'A' and resid 949 through 966
      removed outlier: 3.677A  pdb=" N   SER A 953 " --> pdb=" O   ASN A 949 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 986 through 998
      removed outlier: 4.378A  pdb=" N   SER A 998 " --> pdb=" O   LEU A 994 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 151
      removed outlier: 4.504A  pdb=" N   ILE B 144 " --> pdb=" O   LYS B 140 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   ARG B 145 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN B 149 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 158
    Processing helix  chain 'B' and resid 158 through 166
    Processing helix  chain 'B' and resid 167 through 194
      removed outlier: 3.527A  pdb=" N   VAL B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 211
    Processing helix  chain 'B' and resid 212 through 249
      removed outlier: 3.761A  pdb=" N   SER B 218 " --> pdb=" O   GLU B 214 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA B 232 " --> pdb=" O   ALA B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 277
    Processing helix  chain 'B' and resid 281 through 306
      removed outlier: 4.696A  pdb=" N   VAL B 287 " --> pdb=" O   SER B 283 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU B 288 " --> pdb=" O   LYS B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 316
    Processing helix  chain 'B' and resid 321 through 330
      removed outlier: 4.211A  pdb=" N   VAL B 330 " --> pdb=" O   VAL B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 348
      removed outlier: 3.627A  pdb=" N   ILE B 346 " --> pdb=" O   GLY B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 351
      No H-bonds generated for 'chain 'B' and resid 349 through 351'
    Processing helix  chain 'B' and resid 353 through 361
      removed outlier: 3.826A  pdb=" N   ASN B 359 " --> pdb=" O   ALA B 356 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE B 360 " --> pdb=" O   GLY B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 394
      Proline residue:  B 372  - end of helix
    Processing helix  chain 'B' and resid 418 through 424
    Processing helix  chain 'B' and resid 428 through 434
    Processing helix  chain 'B' and resid 445 through 451
      removed outlier: 3.692A  pdb=" N   MET B 449 " --> pdb=" O   GLN B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 486
      removed outlier: 3.842A  pdb=" N   ILE B 457 " --> pdb=" O   PHE B 453 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU B 470 " --> pdb=" O   LEU B 466 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LYS B 478 " --> pdb=" O   VAL B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 505 through 521
    Processing helix  chain 'B' and resid 524 through 553
      Proline residue:  B 530  - end of helix
    Processing helix  chain 'B' and resid 566 through 585
      removed outlier: 3.631A  pdb=" N   THR B 585 " --> pdb=" O   MET B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 605
      removed outlier: 3.618A  pdb=" N   ALA B 589 " --> pdb=" O   THR B 585 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 618 through 628
      removed outlier: 3.785A  pdb=" N   SER B 626 " --> pdb=" O   ASN B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 665
      removed outlier: 3.749A  pdb=" N   VAL B 659 " --> pdb=" O   ARG B 655 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 703
    Processing helix  chain 'B' and resid 717 through 728
      removed outlier: 4.089A  pdb=" N   LEU B 724 " --> pdb=" O   GLY B 720 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLN B 726 " --> pdb=" O   GLN B 722 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ALA B 727 " --> pdb=" O   ILE B 723 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 730 through 734
    Processing helix  chain 'B' and resid 750 through 767
      removed outlier: 4.266A  pdb=" N   VAL B 754 " --> pdb=" O   HIS B 750 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU B 761 " --> pdb=" O   TYR B 757 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 812 through 820
    Processing helix  chain 'B' and resid 821 through 824
    Processing helix  chain 'B' and resid 841 through 852
      Proline residue:  B 847  - end of helix
    Processing helix  chain 'B' and resid 853 through 859
      removed outlier: 3.997A  pdb=" N   LYS B 858 " --> pdb=" O   ARG B 855 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 872 through 886
      removed outlier: 4.325A  pdb=" N   ALA B 878 " --> pdb=" O   GLN B 874 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 896 through 900
      removed outlier: 3.901A  pdb=" N   ILE B 899 " --> pdb=" O   LEU B 896 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 904 through 914
    Processing helix  chain 'B' and resid 924 through 935
    Processing helix  chain 'B' and resid 949 through 965
    Processing helix  chain 'B' and resid 986 through 998
    Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 713
      removed outlier: 4.337A  pdb=" N   GLY A 741 " --> pdb=" O   LEU A 648 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ARG A 775 " --> pdb=" O   VAL A1005 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 708 through 712
      removed outlier: 3.760A  pdb=" N   PHE B 708 " --> pdb=" O   MET B 672 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   CYS B 645 " --> pdb=" O   ILE B 673 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   GLY B 675 " --> pdb=" O   CYS B 645 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL B 647 " --> pdb=" O   GLY B 675 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   VAL B 677 " --> pdb=" O   VAL B 647 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   LEU B 646 " --> pdb=" O   VAL B 739 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   MET B 774 " --> pdb=" O   VAL B 740 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   ILE B 973 " --> pdb=" O   ILE B1006 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   ILE B1008 " --> pdb=" O   ILE B 973 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ILE B 975 " --> pdb=" O   ILE B1008 " (cutoff:3.500A)

    744 hydrogen bonds defined for protein.
    2151 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: 4.21

  Time building geometry restraints manager: 3.62 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2096
        1.32 -     1.44: 3718
        1.44 -     1.57: 7715
        1.57 -     1.69: 0
        1.69 -     1.81: 124
  Bond restraints: 13653
  Sorted by residual:
  bond pdb=" N   SER B 422 "
       pdb=" CA  SER B 422 "
    ideal  model  delta    sigma   weight residual
    1.456  1.378  0.079 1.31e-02 5.83e+03 3.61e+01
  bond pdb=" CD  GLN B 165 "
       pdb=" OE1 GLN B 165 "
    ideal  model  delta    sigma   weight residual
    1.231  1.329 -0.098 1.90e-02 2.77e+03 2.64e+01
  bond pdb=" CD  GLN A 563 "
       pdb=" OE1 GLN A 563 "
    ideal  model  delta    sigma   weight residual
    1.231  1.328 -0.097 1.90e-02 2.77e+03 2.63e+01
  bond pdb=" CG  ASN B 359 "
       pdb=" OD1 ASN B 359 "
    ideal  model  delta    sigma   weight residual
    1.231  1.327 -0.096 1.90e-02 2.77e+03 2.53e+01
  bond pdb=" C   ASN A 426 "
       pdb=" N   PHE A 427 "
    ideal  model  delta    sigma   weight residual
    1.334  1.272  0.062 1.24e-02 6.50e+03 2.51e+01
  ... (remaining 13648 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 18059
        2.53 -     5.05: 397
        5.05 -     7.58: 66
        7.58 -    10.11: 16
       10.11 -    12.63: 1
  Bond angle restraints: 18539
  Sorted by residual:
  angle pdb=" N   LEU A 836 "
        pdb=" CA  LEU A 836 "
        pdb=" C   LEU A 836 "
      ideal   model   delta    sigma   weight residual
     113.97  101.34   12.63 1.28e+00 6.10e-01 9.74e+01
  angle pdb=" N   ALA A 878 "
        pdb=" CA  ALA A 878 "
        pdb=" C   ALA A 878 "
      ideal   model   delta    sigma   weight residual
     111.28  102.13    9.15 1.09e+00 8.42e-01 7.04e+01
  angle pdb=" N   ASP B 943 "
        pdb=" CA  ASP B 943 "
        pdb=" C   ASP B 943 "
      ideal   model   delta    sigma   weight residual
     112.87  103.14    9.73 1.20e+00 6.94e-01 6.57e+01
  angle pdb=" N   LEU B 780 "
        pdb=" CA  LEU B 780 "
        pdb=" C   LEU B 780 "
      ideal   model   delta    sigma   weight residual
     111.07  103.10    7.97 1.07e+00 8.73e-01 5.55e+01
  angle pdb=" C   LEU A1016 "
        pdb=" CA  LEU A1016 "
        pdb=" CB  LEU A1016 "
      ideal   model   delta    sigma   weight residual
     111.89  101.99    9.90 1.42e+00 4.96e-01 4.86e+01
  ... (remaining 18534 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 7140
       17.59 -    35.18: 729
       35.18 -    52.76: 140
       52.76 -    70.35: 24
       70.35 -    87.94: 6
  Dihedral angle restraints: 8039
    sinusoidal: 3138
      harmonic: 4901
  Sorted by residual:
  dihedral pdb=" CB  CYS B 416 "
           pdb=" SG  CYS B 416 "
           pdb=" SG  CYS B 421 "
           pdb=" CB  CYS B 421 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  151.41  -58.41     1      1.00e+01 1.00e-02 4.57e+01
  dihedral pdb=" CA  GLY A 152 "
           pdb=" C   GLY A 152 "
           pdb=" N   VAL A 153 "
           pdb=" CA  VAL A 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.47  -29.53     0      5.00e+00 4.00e-02 3.49e+01
  dihedral pdb=" CA  GLY B 152 "
           pdb=" C   GLY B 152 "
           pdb=" N   VAL B 153 "
           pdb=" CA  VAL B 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.12  -26.88     0      5.00e+00 4.00e-02 2.89e+01
  ... (remaining 8036 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 1948
       0.085 -    0.169: 147
       0.169 -    0.254: 17
       0.254 -    0.338: 3
       0.338 -    0.423: 3
  Chirality restraints: 2118
  Sorted by residual:
  chirality pdb=" CA  LYS A 784 "
            pdb=" N   LYS A 784 "
            pdb=" C   LYS A 784 "
            pdb=" CB  LYS A 784 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.47e+00
  chirality pdb=" CA  HIS A 750 "
            pdb=" N   HIS A 750 "
            pdb=" C   HIS A 750 "
            pdb=" CB  HIS A 750 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.57e+00
  chirality pdb=" CA  ARG B 334 "
            pdb=" N   ARG B 334 "
            pdb=" C   ARG B 334 "
            pdb=" CB  ARG B 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.97e+00
  ... (remaining 2115 not shown)

  Planarity restraints: 2320
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B1002 "    0.039 5.00e-02 4.00e+02   5.87e-02 5.51e+00
        pdb=" N   PRO B1003 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO B1003 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B1003 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 939 "   -0.014 2.00e-02 2.50e+03   1.37e-02 4.66e+00
        pdb=" CG  TRP B 939 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 939 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 939 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 939 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 939 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 939 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 939 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 939 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 939 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 421 "   -0.010 2.00e-02 2.50e+03   1.98e-02 3.90e+00
        pdb=" C   CYS B 421 "    0.034 2.00e-02 2.50e+03
        pdb=" O   CYS B 421 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER B 422 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 2317 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 2661
        2.76 -     3.29: 14136
        3.29 -     3.83: 23694
        3.83 -     4.36: 28426
        4.36 -     4.90: 45802
  Nonbonded interactions: 114719
  Sorted by model distance:
  nonbonded pdb=" O   SER A 345 "
            pdb=" OG  SER A 533 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   SER B 345 "
            pdb=" OG  SER B 533 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OE2 GLU B 755 "
            pdb=" OG  SER B 987 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OH  TYR A 156 "
            pdb=" OG  SER A 296 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OH  TYR B 156 "
            pdb=" OG  SER B 296 "
     model   vdw
     2.234 3.040
  ... (remaining 114714 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 137 through 959 or (resid 960 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 961 through 989 or (resid 990 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 991 through 1020))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.820
  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:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     29.620
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5882
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      :  0.005   0.101  13657  Z= 0.310
  Angle     :  0.933  12.634  18547  Z= 0.609
  Chirality :  0.051   0.423   2118
  Planarity :  0.005   0.059   2320
  Dihedral  : 14.361  87.938   4887
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 25.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 18.46 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.20), residues: 1696
  helix:  0.74 (0.17), residues: 930
  sheet: -1.64 (0.56), residues: 71
  loop : -2.75 (0.21), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP B 939 
 HIS   0.003   0.001   HIS B 907 
 PHE   0.016   0.001   PHE B 665 
 TYR   0.023   0.001   TYR B 627 
 ARG   0.005   0.000   ARG A 719 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17260 (  744)
  hydrogen bonds       : angle       6.72434 ( 2151)
  SS BOND              : bond        0.00537 (    4)
  SS BOND              : angle       0.77153 (    8)
  covalent geometry    : bond        0.00510 (13653)
  covalent geometry    : angle       0.93353 (18539)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  489 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 472
  time to evaluate  : 1.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 VAL cc_start: 0.7773 (t) cc_final: 0.7407 (t)
REVERT: A  441 ILE cc_start: 0.6761 (tt) cc_final: 0.6041 (tt)
REVERT: A  581 MET cc_start: 0.6009 (ttm) cc_final: 0.5533 (ttm)
REVERT: A  599 LEU cc_start: 0.7811 (mt) cc_final: 0.7549 (mt)
REVERT: A  671 LEU cc_start: 0.6431 (tp) cc_final: 0.6002 (tp)
REVERT: A  776 MET cc_start: 0.3869 (pmm) cc_final: 0.3054 (pmm)
REVERT: B  269 THR cc_start: 0.6876 (m) cc_final: 0.6360 (p)
REVERT: B  505 PRO cc_start: 0.4614 (Cg_endo) cc_final: 0.3654 (Cg_exo)
REVERT: B  642 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6921 (mmm-85)
  outliers start: 17
  outliers final: 5
  residues processed: 486
  average time/residue: 0.2315
  time to fit residues: 163.7680
Evaluate side-chains
  287 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 281
  time to evaluate  : 1.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  686 MET
Chi-restraints excluded: chain A residue  814 LYS
Chi-restraints excluded: chain B residue  642 ARG
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  821 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 143 optimal weight:    7.9990
   chunk 128 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0040
   chunk 133 optimal weight:   10.0000
   chunk 51 optimal weight:    6.9990
   chunk 81 optimal weight:    9.9990
   chunk 99 optimal weight:    9.9990
   chunk 154 optimal weight:    4.9990
   overall best weight:    2.9998

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
A 327 GLN
A 544 ASN
A 566 ASN
A 632 ASN
A 817 GLN
A 891 HIS
** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 999 GLN
A1014 ASN
** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 327 GLN
B 534 ASN
B 566 ASN
B 762 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.081603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.064451 restraints weight = 71381.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.065935 restraints weight = 54030.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.067068 restraints weight = 43444.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  13657  Z= 0.206
  Angle     :  0.836  11.799  18547  Z= 0.425
  Chirality :  0.050   0.285   2118
  Planarity :  0.006   0.112   2320
  Dihedral  :  5.405  48.778   1854
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 27.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 22.73 %
    Favored  : 72.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.20), residues: 1696
  helix:  0.58 (0.17), residues: 946
  sheet: -1.64 (0.54), residues: 86
  loop : -2.34 (0.22), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 699 
 HIS   0.010   0.001   HIS A 234 
 PHE   0.035   0.003   PHE A 341 
 TYR   0.045   0.003   TYR A 627 
 ARG   0.015   0.001   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05294 (  744)
  hydrogen bonds       : angle       5.65136 ( 2151)
  SS BOND              : bond        0.00304 (    4)
  SS BOND              : angle       0.80908 (    8)
  covalent geometry    : bond        0.00448 (13653)
  covalent geometry    : angle       0.83618 (18539)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 303
  time to evaluate  : 1.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 MET cc_start: 0.6820 (ttp) cc_final: 0.5866 (mmm)
REVERT: A  144 ILE cc_start: 0.8617 (mt) cc_final: 0.8283 (tp)
REVERT: A  147 MET cc_start: 0.7871 (mmt) cc_final: 0.7573 (mmt)
REVERT: A  156 TYR cc_start: 0.7686 (m-80) cc_final: 0.7455 (m-10)
REVERT: A  172 TRP cc_start: 0.7956 (m100) cc_final: 0.7564 (m100)
REVERT: A  177 LEU cc_start: 0.9395 (tp) cc_final: 0.9166 (tp)
REVERT: A  328 ASN cc_start: 0.9008 (m-40) cc_final: 0.8674 (m110)
REVERT: A  348 PHE cc_start: 0.8613 (t80) cc_final: 0.8257 (t80)
REVERT: A  509 TYR cc_start: 0.8536 (m-80) cc_final: 0.7888 (m-80)
REVERT: A  581 MET cc_start: 0.8445 (ttm) cc_final: 0.8075 (ttm)
REVERT: A 1018 PHE cc_start: 0.5724 (OUTLIER) cc_final: 0.4602 (t80)
REVERT: B  157 LEU cc_start: 0.8803 (mt) cc_final: 0.8555 (tp)
REVERT: B  187 LEU cc_start: 0.9345 (mt) cc_final: 0.9093 (mt)
REVERT: B  276 LEU cc_start: 0.8673 (mt) cc_final: 0.8044 (pp)
REVERT: B  328 ASN cc_start: 0.8635 (m110) cc_final: 0.8363 (m110)
REVERT: B  505 PRO cc_start: 0.7436 (Cg_endo) cc_final: 0.6939 (Cg_exo)
REVERT: B  540 TYR cc_start: 0.8452 (m-10) cc_final: 0.8219 (m-10)
REVERT: B  548 PHE cc_start: 0.8622 (t80) cc_final: 0.8396 (t80)
REVERT: B  549 HIS cc_start: 0.8867 (OUTLIER) cc_final: 0.8497 (t70)
REVERT: B  642 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7436 (mmm-85)
REVERT: B  658 LEU cc_start: 0.9030 (mp) cc_final: 0.8825 (mp)
REVERT: B  674 CYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8193 (p)
REVERT: B  691 LEU cc_start: 0.9591 (mt) cc_final: 0.9350 (mt)
REVERT: B  774 MET cc_start: 0.6724 (mtp) cc_final: 0.6413 (mtp)
  outliers start: 72
  outliers final: 34
  residues processed: 354
  average time/residue: 0.2192
  time to fit residues: 116.1659
Evaluate side-chains
  304 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 266
  time to evaluate  : 1.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  547 CYS
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  642 ARG
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  849 LEU
Chi-restraints excluded: chain A residue  877 LYS
Chi-restraints excluded: chain A residue 1018 PHE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain B residue  457 ILE
Chi-restraints excluded: chain B residue  534 ASN
Chi-restraints excluded: chain B residue  549 HIS
Chi-restraints excluded: chain B residue  559 ARG
Chi-restraints excluded: chain B residue  561 SER
Chi-restraints excluded: chain B residue  583 LEU
Chi-restraints excluded: chain B residue  642 ARG
Chi-restraints excluded: chain B residue  645 CYS
Chi-restraints excluded: chain B residue  661 PHE
Chi-restraints excluded: chain B residue  670 SER
Chi-restraints excluded: chain B residue  673 ILE
Chi-restraints excluded: chain B residue  674 CYS
Chi-restraints excluded: chain B residue  738 LEU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  865 VAL
Chi-restraints excluded: chain B residue  959 LEU
Chi-restraints excluded: chain B residue  962 ILE
Chi-restraints excluded: chain B residue  965 ASP
Chi-restraints excluded: chain B residue 1001 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 71 optimal weight:   20.0000
   chunk 53 optimal weight:    7.9990
   chunk 126 optimal weight:    5.9990
   chunk 143 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 154 optimal weight:    0.0670
   chunk 138 optimal weight:    7.9990
   chunk 63 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 83 optimal weight:   20.0000
   chunk 142 optimal weight:    7.9990
   overall best weight:    5.0126

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 ASN
A 722 GLN
** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.078817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.060803 restraints weight = 75527.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.062580 restraints weight = 52351.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.063974 restraints weight = 39889.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.4772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  13657  Z= 0.254
  Angle     :  0.798  11.012  18547  Z= 0.415
  Chirality :  0.050   0.256   2118
  Planarity :  0.005   0.083   2320
  Dihedral  :  5.279  35.327   1846
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 29.78
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.37 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 23.29 %
    Favored  : 70.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.20), residues: 1696
  helix:  0.46 (0.16), residues: 945
  sheet: -1.99 (0.46), residues: 101
  loop : -2.19 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 381 
 HIS   0.007   0.001   HIS A 234 
 PHE   0.035   0.003   PHE A 462 
 TYR   0.034   0.002   TYR B 513 
 ARG   0.009   0.001   ARG B 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05045 (  744)
  hydrogen bonds       : angle       5.60747 ( 2151)
  SS BOND              : bond        0.00223 (    4)
  SS BOND              : angle       0.78259 (    8)
  covalent geometry    : bond        0.00521 (13653)
  covalent geometry    : angle       0.79850 (18539)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 269
  time to evaluate  : 1.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 MET cc_start: 0.7507 (ttp) cc_final: 0.6271 (mtp)
REVERT: A  144 ILE cc_start: 0.8984 (mt) cc_final: 0.8695 (tp)
REVERT: A  147 MET cc_start: 0.8514 (mmt) cc_final: 0.8239 (mmt)
REVERT: A  240 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8442 (tm-30)
REVERT: A  328 ASN cc_start: 0.9386 (m-40) cc_final: 0.8996 (m110)
REVERT: A  348 PHE cc_start: 0.9079 (t80) cc_final: 0.8868 (t80)
REVERT: A  377 MET cc_start: 0.8747 (mmt) cc_final: 0.8257 (mpp)
REVERT: A  386 TYR cc_start: 0.9258 (m-80) cc_final: 0.8443 (m-80)
REVERT: A  509 TYR cc_start: 0.8836 (m-80) cc_final: 0.8274 (m-80)
REVERT: A  686 MET cc_start: 0.5966 (ttt) cc_final: 0.5472 (ttp)
REVERT: A  725 MET cc_start: 0.9338 (ptt) cc_final: 0.8719 (ptt)
REVERT: A  774 MET cc_start: 0.5232 (tpt) cc_final: 0.4980 (tpt)
REVERT: A 1018 PHE cc_start: 0.6315 (OUTLIER) cc_final: 0.5264 (t80)
REVERT: B  240 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8831 (tp30)
REVERT: B  276 LEU cc_start: 0.8696 (mt) cc_final: 0.8356 (pp)
REVERT: B  348 PHE cc_start: 0.9419 (t80) cc_final: 0.9109 (t80)
REVERT: B  377 MET cc_start: 0.8699 (mmt) cc_final: 0.8377 (mmt)
REVERT: B  509 TYR cc_start: 0.8407 (m-80) cc_final: 0.8062 (m-80)
REVERT: B  513 TYR cc_start: 0.8772 (t80) cc_final: 0.8572 (t80)
REVERT: B  548 PHE cc_start: 0.8942 (t80) cc_final: 0.8496 (t80)
REVERT: B  642 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7007 (mmm-85)
  outliers start: 82
  outliers final: 43
  residues processed: 321
  average time/residue: 0.2162
  time to fit residues: 105.3043
Evaluate side-chains
  282 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 236
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  465 THR
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  547 CYS
Chi-restraints excluded: chain A residue  583 LEU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  642 ARG
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  849 LEU
Chi-restraints excluded: chain A residue  990 TYR
Chi-restraints excluded: chain A residue 1008 ILE
Chi-restraints excluded: chain A residue 1018 PHE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  225 PHE
Chi-restraints excluded: chain B residue  227 ASN
Chi-restraints excluded: chain B residue  337 ASP
Chi-restraints excluded: chain B residue  350 SER
Chi-restraints excluded: chain B residue  408 THR
Chi-restraints excluded: chain B residue  457 ILE
Chi-restraints excluded: chain B residue  465 THR
Chi-restraints excluded: chain B residue  534 ASN
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  549 HIS
Chi-restraints excluded: chain B residue  559 ARG
Chi-restraints excluded: chain B residue  642 ARG
Chi-restraints excluded: chain B residue  645 CYS
Chi-restraints excluded: chain B residue  661 PHE
Chi-restraints excluded: chain B residue  671 LEU
Chi-restraints excluded: chain B residue  674 CYS
Chi-restraints excluded: chain B residue  765 PHE
Chi-restraints excluded: chain B residue  772 CYS
Chi-restraints excluded: chain B residue  785 MET
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  962 ILE
Chi-restraints excluded: chain B residue  975 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 137 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9980
   chunk 138 optimal weight:    0.6980
   chunk 1 optimal weight:    5.9990
   chunk 106 optimal weight:    1.9990
   chunk 143 optimal weight:    0.0970
   chunk 58 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0070
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 722 GLN
A 762 HIS
** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.081521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.063464 restraints weight = 70993.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.065344 restraints weight = 48862.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.066774 restraints weight = 36941.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.5162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13657  Z= 0.153
  Angle     :  0.812  12.910  18547  Z= 0.390
  Chirality :  0.048   0.265   2118
  Planarity :  0.005   0.073   2320
  Dihedral  :  5.153  37.473   1845
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 23.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 24.69 %
    Favored  : 71.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.20), residues: 1696
  helix:  0.58 (0.17), residues: 952
  sheet: -1.53 (0.49), residues: 95
  loop : -2.01 (0.23), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.001   TRP B 151 
 HIS   0.007   0.001   HIS A 234 
 PHE   0.025   0.002   PHE A 325 
 TYR   0.039   0.002   TYR A 156 
 ARG   0.005   0.001   ARG A1009 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04429 (  744)
  hydrogen bonds       : angle       5.29807 ( 2151)
  SS BOND              : bond        0.00257 (    4)
  SS BOND              : angle       0.71986 (    8)
  covalent geometry    : bond        0.00335 (13653)
  covalent geometry    : angle       0.81178 (18539)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 269
  time to evaluate  : 1.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 MET cc_start: 0.7393 (ttp) cc_final: 0.6240 (mmm)
REVERT: A  144 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8476 (tp)
REVERT: A  147 MET cc_start: 0.8494 (mmt) cc_final: 0.8209 (mmt)
REVERT: A  328 ASN cc_start: 0.9368 (m-40) cc_final: 0.9086 (m110)
REVERT: A  343 MET cc_start: 0.8969 (mmt) cc_final: 0.8686 (mmt)
REVERT: A  377 MET cc_start: 0.8806 (mmt) cc_final: 0.8340 (mpp)
REVERT: A  386 TYR cc_start: 0.9159 (m-80) cc_final: 0.8499 (m-80)
REVERT: A  509 TYR cc_start: 0.8800 (m-80) cc_final: 0.8364 (m-80)
REVERT: A  686 MET cc_start: 0.6244 (ttt) cc_final: 0.5805 (ttp)
REVERT: A  700 LEU cc_start: 0.9674 (mp) cc_final: 0.9469 (pp)
REVERT: A  725 MET cc_start: 0.9325 (ptt) cc_final: 0.8577 (ptt)
REVERT: A  835 TRP cc_start: 0.6782 (m100) cc_final: 0.6412 (m100)
REVERT: A  872 MET cc_start: 0.4070 (tpt) cc_final: 0.2303 (mmm)
REVERT: A 1018 PHE cc_start: 0.6479 (OUTLIER) cc_final: 0.6212 (m-80)
REVERT: B  165 GLN cc_start: 0.8381 (tp40) cc_final: 0.7755 (tp-100)
REVERT: B  233 MET cc_start: 0.9424 (tmm) cc_final: 0.9160 (tmm)
REVERT: B  240 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8772 (tp30)
REVERT: B  267 SER cc_start: 0.8888 (m) cc_final: 0.8626 (p)
REVERT: B  276 LEU cc_start: 0.8571 (mt) cc_final: 0.8361 (pp)
REVERT: B  348 PHE cc_start: 0.9410 (t80) cc_final: 0.9076 (t80)
REVERT: B  509 TYR cc_start: 0.8249 (m-80) cc_final: 0.7885 (m-80)
REVERT: B  513 TYR cc_start: 0.8762 (t80) cc_final: 0.8427 (t80)
REVERT: B  548 PHE cc_start: 0.8915 (t80) cc_final: 0.8531 (t80)
REVERT: B  595 VAL cc_start: 0.9234 (t) cc_final: 0.9021 (m)
REVERT: B  596 VAL cc_start: 0.8722 (t) cc_final: 0.8458 (t)
REVERT: B  642 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7200 (mmm-85)
REVERT: B  834 TYR cc_start: 0.8115 (m-80) cc_final: 0.7813 (m-80)
  outliers start: 61
  outliers final: 36
  residues processed: 308
  average time/residue: 0.2036
  time to fit residues: 96.4564
Evaluate side-chains
  283 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 244
  time to evaluate  : 1.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  547 CYS
Chi-restraints excluded: chain A residue  642 ARG
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  849 LEU
Chi-restraints excluded: chain A residue  974 VAL
Chi-restraints excluded: chain A residue 1008 ILE
Chi-restraints excluded: chain A residue 1018 PHE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  227 ASN
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  337 ASP
Chi-restraints excluded: chain B residue  383 THR
Chi-restraints excluded: chain B residue  457 ILE
Chi-restraints excluded: chain B residue  495 PHE
Chi-restraints excluded: chain B residue  528 ILE
Chi-restraints excluded: chain B residue  534 ASN
Chi-restraints excluded: chain B residue  549 HIS
Chi-restraints excluded: chain B residue  559 ARG
Chi-restraints excluded: chain B residue  642 ARG
Chi-restraints excluded: chain B residue  673 ILE
Chi-restraints excluded: chain B residue  677 VAL
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  994 LEU
Chi-restraints excluded: chain B residue 1005 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 24 optimal weight:    8.9990
   chunk 168 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 146 optimal weight:    1.9990
   chunk 106 optimal weight:    0.8980
   chunk 8 optimal weight:    6.9990
   chunk 151 optimal weight:    9.9990
   chunk 101 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 426 ASN
** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 891 HIS
** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.080753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.062733 restraints weight = 71364.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.064597 restraints weight = 49345.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.066055 restraints weight = 37340.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6350
moved from start:          0.5536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  13657  Z= 0.151
  Angle     :  0.797  10.929  18547  Z= 0.385
  Chirality :  0.048   0.340   2118
  Planarity :  0.005   0.051   2320
  Dihedral  :  5.106  35.858   1845
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 23.46
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.60 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 27.76 %
    Favored  : 68.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.20), residues: 1696
  helix:  0.58 (0.17), residues: 957
  sheet: -1.31 (0.50), residues: 94
  loop : -2.02 (0.23), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP B 151 
 HIS   0.006   0.001   HIS B 234 
 PHE   0.032   0.002   PHE A 348 
 TYR   0.033   0.002   TYR B 627 
 ARG   0.008   0.000   ARG B 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04301 (  744)
  hydrogen bonds       : angle       5.33105 ( 2151)
  SS BOND              : bond        0.00852 (    4)
  SS BOND              : angle       1.14177 (    8)
  covalent geometry    : bond        0.00337 (13653)
  covalent geometry    : angle       0.79653 (18539)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 257
  time to evaluate  : 1.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 MET cc_start: 0.6719 (ttp) cc_final: 0.6165 (mmm)
REVERT: A  144 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8403 (tp)
REVERT: A  328 ASN cc_start: 0.9093 (m-40) cc_final: 0.8704 (m110)
REVERT: A  343 MET cc_start: 0.8946 (mmt) cc_final: 0.8545 (mmt)
REVERT: A  348 PHE cc_start: 0.8790 (t80) cc_final: 0.8460 (t80)
REVERT: A  377 MET cc_start: 0.8840 (mmt) cc_final: 0.8589 (mpp)
REVERT: A  386 TYR cc_start: 0.9457 (m-80) cc_final: 0.8868 (m-80)
REVERT: A  416 CYS cc_start: 0.0031 (OUTLIER) cc_final: -0.0386 (m)
REVERT: A  441 ILE cc_start: 0.8484 (tp) cc_final: 0.8277 (pt)
REVERT: A  509 TYR cc_start: 0.8809 (m-80) cc_final: 0.8523 (m-80)
REVERT: A  581 MET cc_start: 0.9196 (ttm) cc_final: 0.8955 (tmm)
REVERT: A  642 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6256 (mmm160)
REVERT: A  686 MET cc_start: 0.5915 (ttt) cc_final: 0.5400 (ttp)
REVERT: A  725 MET cc_start: 0.9590 (ptt) cc_final: 0.9265 (ptt)
REVERT: A  835 TRP cc_start: 0.7056 (m100) cc_final: 0.6778 (m100)
REVERT: A  872 MET cc_start: 0.5101 (tpt) cc_final: 0.3898 (mmm)
REVERT: B  157 LEU cc_start: 0.8649 (tp) cc_final: 0.8257 (tp)
REVERT: B  348 PHE cc_start: 0.9163 (t80) cc_final: 0.8903 (t80)
REVERT: B  509 TYR cc_start: 0.8631 (m-80) cc_final: 0.8297 (m-80)
REVERT: B  513 TYR cc_start: 0.8686 (t80) cc_final: 0.8383 (t80)
REVERT: B  596 VAL cc_start: 0.8409 (t) cc_final: 0.8181 (t)
REVERT: B  642 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.6158 (mmm-85)
REVERT: B  725 MET cc_start: 0.9327 (ppp) cc_final: 0.8958 (ppp)
REVERT: B  776 MET cc_start: 0.8921 (tpp) cc_final: 0.8204 (tmm)
  outliers start: 54
  outliers final: 36
  residues processed: 295
  average time/residue: 0.2126
  time to fit residues: 95.5992
Evaluate side-chains
  278 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 238
  time to evaluate  : 1.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  547 CYS
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  642 ARG
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  849 LEU
Chi-restraints excluded: chain A residue 1008 ILE
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  337 ASP
Chi-restraints excluded: chain B residue  457 ILE
Chi-restraints excluded: chain B residue  495 PHE
Chi-restraints excluded: chain B residue  534 ASN
Chi-restraints excluded: chain B residue  549 HIS
Chi-restraints excluded: chain B residue  559 ARG
Chi-restraints excluded: chain B residue  642 ARG
Chi-restraints excluded: chain B residue  673 ILE
Chi-restraints excluded: chain B residue  677 VAL
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  975 ILE
Chi-restraints excluded: chain B residue  977 LEU
Chi-restraints excluded: chain B residue  994 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 20 optimal weight:    0.1980
   chunk 85 optimal weight:   20.0000
   chunk 118 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 127 optimal weight:    0.0010
   chunk 159 optimal weight:    5.9990
   chunk 106 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 124 optimal weight:    0.9990
   overall best weight:    1.0392

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

Flipped N/Q/H residues before XYZ refinement:
** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 640 ASN
** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.080867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.062961 restraints weight = 73371.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.064770 restraints weight = 50546.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.066214 restraints weight = 38327.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6749
moved from start:          0.5883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  13657  Z= 0.146
  Angle     :  0.799  13.883  18547  Z= 0.382
  Chirality :  0.049   0.370   2118
  Planarity :  0.004   0.048   2320
  Dihedral  :  5.018  34.713   1845
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 22.60
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.60 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 27.83 %
    Favored  : 67.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.20), residues: 1696
  helix:  0.55 (0.17), residues: 961
  sheet: -1.23 (0.51), residues: 94
  loop : -1.99 (0.24), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.001   TRP B 151 
 HIS   0.005   0.001   HIS B 637 
 PHE   0.035   0.002   PHE A 325 
 TYR   0.022   0.002   TYR B 627 
 ARG   0.003   0.000   ARG A1009 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04211 (  744)
  hydrogen bonds       : angle       5.29212 ( 2151)
  SS BOND              : bond        0.00258 (    4)
  SS BOND              : angle       0.81430 (    8)
  covalent geometry    : bond        0.00332 (13653)
  covalent geometry    : angle       0.79861 (18539)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 255
  time to evaluate  : 1.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 VAL cc_start: 0.8632 (t) cc_final: 0.8354 (t)
REVERT: A  143 MET cc_start: 0.6838 (ttp) cc_final: 0.6613 (mmm)
REVERT: A  144 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8472 (tp)
REVERT: A  156 TYR cc_start: 0.8926 (m-10) cc_final: 0.8564 (m-10)
REVERT: A  328 ASN cc_start: 0.9318 (m-40) cc_final: 0.8863 (m-40)
REVERT: A  343 MET cc_start: 0.9139 (mmt) cc_final: 0.8699 (mmt)
REVERT: A  348 PHE cc_start: 0.8874 (t80) cc_final: 0.8325 (t80)
REVERT: A  377 MET cc_start: 0.8861 (mmt) cc_final: 0.8642 (mpp)
REVERT: A  386 TYR cc_start: 0.9454 (m-80) cc_final: 0.8911 (m-80)
REVERT: A  400 ASP cc_start: 0.8255 (p0) cc_final: 0.7695 (p0)
REVERT: A  447 MET cc_start: 0.9142 (ppp) cc_final: 0.8309 (ppp)
REVERT: A  509 TYR cc_start: 0.8852 (m-80) cc_final: 0.8553 (m-80)
REVERT: A  536 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.8862 (t80)
REVERT: A  581 MET cc_start: 0.9362 (ttm) cc_final: 0.9077 (tmm)
REVERT: A  686 MET cc_start: 0.6297 (ttt) cc_final: 0.5650 (ttp)
REVERT: A  725 MET cc_start: 0.9668 (ptt) cc_final: 0.9255 (ptt)
REVERT: A  835 TRP cc_start: 0.7042 (m100) cc_final: 0.6649 (m100)
REVERT: A  872 MET cc_start: 0.4727 (tpt) cc_final: 0.3526 (mmm)
REVERT: A 1018 PHE cc_start: 0.6154 (OUTLIER) cc_final: 0.5847 (m-80)
REVERT: B  151 TRP cc_start: 0.7522 (m-90) cc_final: 0.6750 (m-90)
REVERT: B  157 LEU cc_start: 0.8700 (tp) cc_final: 0.8482 (tp)
REVERT: B  165 GLN cc_start: 0.8450 (tp-100) cc_final: 0.8180 (tp-100)
REVERT: B  221 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8808 (mp)
REVERT: B  348 PHE cc_start: 0.9302 (t80) cc_final: 0.9009 (t80)
REVERT: B  377 MET cc_start: 0.8962 (mmt) cc_final: 0.8577 (ttt)
REVERT: B  513 TYR cc_start: 0.8728 (t80) cc_final: 0.8346 (t80)
REVERT: B  642 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6534 (mmm-85)
REVERT: B  725 MET cc_start: 0.9376 (ppp) cc_final: 0.9004 (ppp)
REVERT: B  774 MET cc_start: 0.8068 (mtt) cc_final: 0.7754 (mmm)
  outliers start: 65
  outliers final: 42
  residues processed: 299
  average time/residue: 0.2175
  time to fit residues: 100.4106
Evaluate side-chains
  278 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 231
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  323 ASP
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  547 CYS
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  849 LEU
Chi-restraints excluded: chain A residue  974 VAL
Chi-restraints excluded: chain A residue 1008 ILE
Chi-restraints excluded: chain A residue 1018 PHE
Chi-restraints excluded: chain B residue  149 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  337 ASP
Chi-restraints excluded: chain B residue  457 ILE
Chi-restraints excluded: chain B residue  495 PHE
Chi-restraints excluded: chain B residue  528 ILE
Chi-restraints excluded: chain B residue  534 ASN
Chi-restraints excluded: chain B residue  549 HIS
Chi-restraints excluded: chain B residue  559 ARG
Chi-restraints excluded: chain B residue  642 ARG
Chi-restraints excluded: chain B residue  673 ILE
Chi-restraints excluded: chain B residue  677 VAL
Chi-restraints excluded: chain B residue  708 PHE
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  834 TYR
Chi-restraints excluded: chain B residue  975 ILE
Chi-restraints excluded: chain B residue  979 ILE
Chi-restraints excluded: chain B residue  994 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 137 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0770
   chunk 11 optimal weight:    1.9990
   chunk 158 optimal weight:    0.9990
   chunk 111 optimal weight:   10.0000
   chunk 72 optimal weight:    9.9990
   chunk 59 optimal weight:    0.8980
   chunk 141 optimal weight:   10.0000
   chunk 119 optimal weight:    9.9990
   chunk 69 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   overall best weight:    0.9542

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

Flipped N/Q/H residues before XYZ refinement:
** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 442 ASN
** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 299 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.079855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.063471 restraints weight = 73839.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.064842 restraints weight = 56259.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.065868 restraints weight = 45760.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.6113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  13657  Z= 0.141
  Angle     :  0.787  13.047  18547  Z= 0.378
  Chirality :  0.048   0.365   2118
  Planarity :  0.004   0.049   2320
  Dihedral  :  4.966  33.814   1845
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 21.86
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.19 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 29.79 %
    Favored  : 66.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.20), residues: 1696
  helix:  0.54 (0.17), residues: 966
  sheet: -1.10 (0.52), residues: 94
  loop : -1.95 (0.24), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP B 151 
 HIS   0.005   0.001   HIS B 637 
 PHE   0.070   0.002   PHE A 462 
 TYR   0.020   0.002   TYR B 627 
 ARG   0.010   0.000   ARG A 685 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04170 (  744)
  hydrogen bonds       : angle       5.20916 ( 2151)
  SS BOND              : bond        0.00281 (    4)
  SS BOND              : angle       0.81624 (    8)
  covalent geometry    : bond        0.00318 (13653)
  covalent geometry    : angle       0.78690 (18539)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 255
  time to evaluate  : 1.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 MET cc_start: 0.7785 (mmt) cc_final: 0.7523 (mmt)
REVERT: A  386 TYR cc_start: 0.8515 (m-80) cc_final: 0.8133 (m-80)
REVERT: A  400 ASP cc_start: 0.7570 (p0) cc_final: 0.6772 (p0)
REVERT: A  447 MET cc_start: 0.9296 (ppp) cc_final: 0.8586 (ppp)
REVERT: A  457 ILE cc_start: 0.8935 (mp) cc_final: 0.8663 (pt)
REVERT: A  536 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8718 (t80)
REVERT: A  725 MET cc_start: 0.8857 (ptt) cc_final: 0.8214 (ptt)
REVERT: A  835 TRP cc_start: 0.6525 (m100) cc_final: 0.6175 (m100)
REVERT: A  872 MET cc_start: 0.3576 (tpt) cc_final: 0.2116 (mmm)
REVERT: B  143 MET cc_start: 0.5938 (mmm) cc_final: 0.5651 (tpt)
REVERT: B  147 MET cc_start: 0.6732 (mmt) cc_final: 0.6266 (mmt)
REVERT: B  165 GLN cc_start: 0.7915 (tp-100) cc_final: 0.7499 (tp-100)
REVERT: B  221 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8921 (mp)
REVERT: B  513 TYR cc_start: 0.8778 (t80) cc_final: 0.8318 (t80)
REVERT: B  540 TYR cc_start: 0.8501 (m-10) cc_final: 0.8273 (m-10)
REVERT: B  642 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7590 (mmm-85)
  outliers start: 57
  outliers final: 47
  residues processed: 298
  average time/residue: 0.2031
  time to fit residues: 93.7364
Evaluate side-chains
  284 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 234
  time to evaluate  : 1.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  323 ASP
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  547 CYS
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  849 LEU
Chi-restraints excluded: chain A residue  940 LYS
Chi-restraints excluded: chain A residue  974 VAL
Chi-restraints excluded: chain A residue 1008 ILE
Chi-restraints excluded: chain B residue  149 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  337 ASP
Chi-restraints excluded: chain B residue  457 ILE
Chi-restraints excluded: chain B residue  495 PHE
Chi-restraints excluded: chain B residue  534 ASN
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  549 HIS
Chi-restraints excluded: chain B residue  559 ARG
Chi-restraints excluded: chain B residue  642 ARG
Chi-restraints excluded: chain B residue  673 ILE
Chi-restraints excluded: chain B residue  677 VAL
Chi-restraints excluded: chain B residue  708 PHE
Chi-restraints excluded: chain B residue  772 CYS
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  834 TYR
Chi-restraints excluded: chain B residue  865 VAL
Chi-restraints excluded: chain B residue  975 ILE
Chi-restraints excluded: chain B residue  977 LEU
Chi-restraints excluded: chain B residue  994 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 69 optimal weight:    8.9990
   chunk 156 optimal weight:    4.9990
   chunk 90 optimal weight:   10.0000
   chunk 34 optimal weight:    8.9990
   chunk 150 optimal weight:    5.9990
   chunk 128 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 24 optimal weight:    0.7980
   chunk 47 optimal weight:    7.9990
   chunk 66 optimal weight:    7.9990
   overall best weight:    5.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 445 GLN
A 668 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.074787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.058993 restraints weight = 77551.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.060156 restraints weight = 60291.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.061038 restraints weight = 49777.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.6593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  13657  Z= 0.248
  Angle     :  0.847  14.518  18547  Z= 0.428
  Chirality :  0.050   0.376   2118
  Planarity :  0.005   0.047   2320
  Dihedral  :  5.257  33.982   1845
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 30.78
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.37 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 29.23 %
    Favored  : 65.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.20), residues: 1696
  helix:  0.28 (0.16), residues: 959
  sheet: -1.37 (0.49), residues: 102
  loop : -1.88 (0.24), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.078   0.002   TRP B 151 
 HIS   0.007   0.001   HIS B 234 
 PHE   0.065   0.003   PHE A 348 
 TYR   0.028   0.003   TYR A 443 
 ARG   0.015   0.001   ARG B 910 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04676 (  744)
  hydrogen bonds       : angle       5.65001 ( 2151)
  SS BOND              : bond        0.00238 (    4)
  SS BOND              : angle       0.89952 (    8)
  covalent geometry    : bond        0.00528 (13653)
  covalent geometry    : angle       0.84743 (18539)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 224
  time to evaluate  : 1.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 MET cc_start: 0.7930 (mmm) cc_final: 0.6924 (mmm)
REVERT: A  147 MET cc_start: 0.7940 (mmt) cc_final: 0.7696 (mmt)
REVERT: A  386 TYR cc_start: 0.8630 (m-80) cc_final: 0.8136 (m-80)
REVERT: A  416 CYS cc_start: 0.0164 (OUTLIER) cc_final: -0.0452 (m)
REVERT: A  509 TYR cc_start: 0.8412 (m-80) cc_final: 0.8097 (m-10)
REVERT: A  536 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8751 (t80)
REVERT: A  725 MET cc_start: 0.9015 (ptt) cc_final: 0.8651 (ptt)
REVERT: A  835 TRP cc_start: 0.6460 (m100) cc_final: 0.6191 (m100)
REVERT: A  872 MET cc_start: 0.3694 (tpt) cc_final: 0.2544 (mmm)
REVERT: B  165 GLN cc_start: 0.8143 (tp-100) cc_final: 0.7670 (tp-100)
REVERT: B  221 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8968 (mt)
REVERT: B  290 PHE cc_start: 0.8554 (t80) cc_final: 0.8341 (t80)
REVERT: B  513 TYR cc_start: 0.8779 (t80) cc_final: 0.8326 (t80)
REVERT: B  548 PHE cc_start: 0.8733 (t80) cc_final: 0.8457 (t80)
REVERT: B  642 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7653 (mmm-85)
  outliers start: 73
  outliers final: 52
  residues processed: 278
  average time/residue: 0.2103
  time to fit residues: 90.1794
Evaluate side-chains
  270 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 214
  time to evaluate  : 1.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  323 ASP
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  547 CYS
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  668 ASN
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  849 LEU
Chi-restraints excluded: chain A residue  940 LYS
Chi-restraints excluded: chain A residue  990 TYR
Chi-restraints excluded: chain A residue 1008 ILE
Chi-restraints excluded: chain B residue  149 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  225 PHE
Chi-restraints excluded: chain B residue  227 ASN
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  337 ASP
Chi-restraints excluded: chain B residue  340 PHE
Chi-restraints excluded: chain B residue  457 ILE
Chi-restraints excluded: chain B residue  495 PHE
Chi-restraints excluded: chain B residue  534 ASN
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  549 HIS
Chi-restraints excluded: chain B residue  642 ARG
Chi-restraints excluded: chain B residue  673 ILE
Chi-restraints excluded: chain B residue  674 CYS
Chi-restraints excluded: chain B residue  677 VAL
Chi-restraints excluded: chain B residue  708 PHE
Chi-restraints excluded: chain B residue  772 CYS
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  865 VAL
Chi-restraints excluded: chain B residue  962 ILE
Chi-restraints excluded: chain B residue  975 ILE
Chi-restraints excluded: chain B residue  977 LEU
Chi-restraints excluded: chain B residue  979 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 109 optimal weight:    7.9990
   chunk 81 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 165 optimal weight:   20.0000
   chunk 67 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   chunk 164 optimal weight:    6.9990
   chunk 134 optimal weight:    0.0070
   chunk 8 optimal weight:    9.9990
   chunk 135 optimal weight:    8.9990
   chunk 127 optimal weight:    9.9990
   overall best weight:    2.3202

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 668 ASN
A 891 HIS
** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.076620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.060687 restraints weight = 75769.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.061901 restraints weight = 58528.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.062813 restraints weight = 48223.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.6773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  13657  Z= 0.166
  Angle     :  0.853  14.852  18547  Z= 0.413
  Chirality :  0.050   0.362   2118
  Planarity :  0.005   0.047   2320
  Dihedral  :  5.227  35.590   1845
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 25.06
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.31 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 30.91 %
    Favored  : 65.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.20), residues: 1696
  helix:  0.33 (0.16), residues: 964
  sheet: -1.23 (0.49), residues: 102
  loop : -1.85 (0.24), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.084   0.002   TRP B 151 
 HIS   0.006   0.001   HIS B 234 
 PHE   0.051   0.002   PHE A 348 
 TYR   0.023   0.002   TYR B 627 
 ARG   0.014   0.001   ARG B 719 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04450 (  744)
  hydrogen bonds       : angle       5.53199 ( 2151)
  SS BOND              : bond        0.00259 (    4)
  SS BOND              : angle       0.86880 (    8)
  covalent geometry    : bond        0.00376 (13653)
  covalent geometry    : angle       0.85273 (18539)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 232
  time to evaluate  : 1.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 MET cc_start: 0.7547 (mmm) cc_final: 0.6271 (mmt)
REVERT: A  147 MET cc_start: 0.7971 (mmt) cc_final: 0.7634 (mmt)
REVERT: A  172 TRP cc_start: 0.8799 (m100) cc_final: 0.8121 (m100)
REVERT: A  386 TYR cc_start: 0.8486 (m-80) cc_final: 0.8076 (m-80)
REVERT: A  416 CYS cc_start: -0.0505 (OUTLIER) cc_final: -0.1040 (m)
REVERT: A  509 TYR cc_start: 0.8393 (m-80) cc_final: 0.8071 (m-10)
REVERT: A  536 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8678 (t80)
REVERT: A  686 MET cc_start: 0.6651 (ttt) cc_final: 0.6080 (ttp)
REVERT: A  725 MET cc_start: 0.8949 (ptt) cc_final: 0.8332 (ptt)
REVERT: A  872 MET cc_start: 0.3486 (tpt) cc_final: 0.2367 (mmm)
REVERT: B  165 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7612 (tp-100)
REVERT: B  221 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8965 (mt)
REVERT: B  290 PHE cc_start: 0.8573 (t80) cc_final: 0.8335 (t80)
REVERT: B  513 TYR cc_start: 0.8696 (t80) cc_final: 0.8245 (t80)
REVERT: B  548 PHE cc_start: 0.8642 (t80) cc_final: 0.8406 (t80)
REVERT: B  581 MET cc_start: 0.9254 (ppp) cc_final: 0.8819 (ppp)
REVERT: B  642 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7544 (mmm-85)
REVERT: B  725 MET cc_start: 0.9024 (ppp) cc_final: 0.8578 (ppp)
  outliers start: 55
  outliers final: 42
  residues processed: 274
  average time/residue: 0.1991
  time to fit residues: 85.9684
Evaluate side-chains
  273 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 227
  time to evaluate  : 1.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  323 ASP
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  547 CYS
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  668 ASN
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  940 LYS
Chi-restraints excluded: chain A residue 1008 ILE
Chi-restraints excluded: chain B residue  149 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  225 PHE
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  337 ASP
Chi-restraints excluded: chain B residue  340 PHE
Chi-restraints excluded: chain B residue  457 ILE
Chi-restraints excluded: chain B residue  495 PHE
Chi-restraints excluded: chain B residue  534 ASN
Chi-restraints excluded: chain B residue  549 HIS
Chi-restraints excluded: chain B residue  642 ARG
Chi-restraints excluded: chain B residue  673 ILE
Chi-restraints excluded: chain B residue  677 VAL
Chi-restraints excluded: chain B residue  708 PHE
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  834 TYR
Chi-restraints excluded: chain B residue  865 VAL
Chi-restraints excluded: chain B residue  975 ILE
Chi-restraints excluded: chain B residue  977 LEU
Chi-restraints excluded: chain B residue  979 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 107 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 69 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 112 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0980
   chunk 130 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0050
   chunk 20 optimal weight:    0.9980
   overall best weight:    1.0198

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 668 ASN
A 891 HIS
** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.077558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.061667 restraints weight = 75809.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.062950 restraints weight = 58190.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.063914 restraints weight = 47495.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.6907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  13657  Z= 0.157
  Angle     :  0.887  15.017  18547  Z= 0.420
  Chirality :  0.051   0.365   2118
  Planarity :  0.005   0.046   2320
  Dihedral  :  5.184  37.948   1845
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 23.61
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.07 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 31.61 %
    Favored  : 65.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.20), residues: 1696
  helix:  0.39 (0.17), residues: 964
  sheet: -0.94 (0.52), residues: 92
  loop : -1.83 (0.24), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.088   0.002   TRP B 151 
 HIS   0.007   0.001   HIS B 234 
 PHE   0.055   0.002   PHE A 348 
 TYR   0.024   0.002   TYR B 627 
 ARG   0.007   0.001   ARG A 685 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04402 (  744)
  hydrogen bonds       : angle       5.44866 ( 2151)
  SS BOND              : bond        0.00283 (    4)
  SS BOND              : angle       0.88107 (    8)
  covalent geometry    : bond        0.00357 (13653)
  covalent geometry    : angle       0.88731 (18539)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 242
  time to evaluate  : 1.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 MET cc_start: 0.7335 (mmm) cc_final: 0.5968 (mmt)
REVERT: A  147 MET cc_start: 0.7924 (mmt) cc_final: 0.7665 (mmt)
REVERT: A  172 TRP cc_start: 0.8733 (m100) cc_final: 0.8077 (m100)
REVERT: A  240 GLU cc_start: 0.8333 (tt0) cc_final: 0.7520 (tm-30)
REVERT: A  386 TYR cc_start: 0.8440 (m-80) cc_final: 0.8072 (m-80)
REVERT: A  416 CYS cc_start: -0.0614 (OUTLIER) cc_final: -0.1147 (m)
REVERT: A  509 TYR cc_start: 0.8454 (m-80) cc_final: 0.8121 (m-10)
REVERT: A  536 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8635 (t80)
REVERT: A  686 MET cc_start: 0.6763 (ttt) cc_final: 0.6247 (ttp)
REVERT: A  725 MET cc_start: 0.8946 (ptt) cc_final: 0.8293 (ptt)
REVERT: A  872 MET cc_start: 0.3256 (tpt) cc_final: 0.2186 (mmm)
REVERT: B  165 GLN cc_start: 0.8002 (tp-100) cc_final: 0.7639 (tp-100)
REVERT: B  221 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8934 (mt)
REVERT: B  290 PHE cc_start: 0.8543 (t80) cc_final: 0.8322 (t80)
REVERT: B  513 TYR cc_start: 0.8718 (t80) cc_final: 0.8246 (t80)
REVERT: B  581 MET cc_start: 0.9246 (ppp) cc_final: 0.8815 (ppp)
REVERT: B  642 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7666 (mmm-85)
REVERT: B  725 MET cc_start: 0.9023 (ppp) cc_final: 0.8640 (ppp)
REVERT: B  774 MET cc_start: 0.7947 (mmm) cc_final: 0.7635 (mtt)
  outliers start: 46
  outliers final: 36
  residues processed: 276
  average time/residue: 0.2089
  time to fit residues: 89.9608
Evaluate side-chains
  273 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 233
  time to evaluate  : 1.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  323 ASP
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  547 CYS
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  940 LYS
Chi-restraints excluded: chain A residue 1008 ILE
Chi-restraints excluded: chain B residue  149 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  225 PHE
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  337 ASP
Chi-restraints excluded: chain B residue  340 PHE
Chi-restraints excluded: chain B residue  534 ASN
Chi-restraints excluded: chain B residue  549 HIS
Chi-restraints excluded: chain B residue  642 ARG
Chi-restraints excluded: chain B residue  673 ILE
Chi-restraints excluded: chain B residue  677 VAL
Chi-restraints excluded: chain B residue  708 PHE
Chi-restraints excluded: chain B residue  772 CYS
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  858 LYS
Chi-restraints excluded: chain B residue  959 LEU
Chi-restraints excluded: chain B residue  975 ILE
Chi-restraints excluded: chain B residue  977 LEU
Chi-restraints excluded: chain B residue  979 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 22 optimal weight:   30.0000
   chunk 2 optimal weight:    3.9990
   chunk 168 optimal weight:   10.0000
   chunk 116 optimal weight:    0.1980
   chunk 12 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 55 optimal weight:    7.9990
   chunk 78 optimal weight:    5.9990
   chunk 77 optimal weight:    0.0070
   chunk 66 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    2.0002

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 891 HIS
** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.078178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.062168 restraints weight = 75628.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.063290 restraints weight = 59848.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.064161 restraints weight = 50192.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.7057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  13657  Z= 0.159
  Angle     :  0.883  17.345  18547  Z= 0.419
  Chirality :  0.051   0.368   2118
  Planarity :  0.005   0.047   2320
  Dihedral  :  5.178  37.121   1845
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 23.87
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.01 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 31.89 %
    Favored  : 64.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.20), residues: 1696
  helix:  0.37 (0.17), residues: 965
  sheet: -0.83 (0.55), residues: 85
  loop : -1.81 (0.24), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.082   0.002   TRP B 151 
 HIS   0.008   0.001   HIS B 234 
 PHE   0.055   0.002   PHE A 348 
 TYR   0.023   0.002   TYR B 627 
 ARG   0.014   0.001   ARG A 685 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04362 (  744)
  hydrogen bonds       : angle       5.47001 ( 2151)
  SS BOND              : bond        0.00266 (    4)
  SS BOND              : angle       0.92626 (    8)
  covalent geometry    : bond        0.00366 (13653)
  covalent geometry    : angle       0.88327 (18539)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4776.34 seconds
wall clock time: 84 minutes 22.12 seconds (5062.12 seconds total)