Starting phenix.real_space_refine
on Wed Mar  4 06:31:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t56_25696/03_2026/7t56_25696.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t56_25696/03_2026/7t56_25696.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t56_25696/03_2026/7t56_25696.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t56_25696/03_2026/7t56_25696.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t56_25696/03_2026/7t56_25696.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t56_25696/03_2026/7t56_25696.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.033
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      60      5.16       5
     C    7382      2.51       5
     N    1870      2.21       5
     O    2140      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11460
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 715, 5581
          Classifications: {'peptide': 715}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701}
    Chain: "C"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 117
          Classifications: {'peptide': 17}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 16}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 5581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 715, 5581
          Classifications: {'peptide': 715}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701}
    Chain: "D"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 117
          Classifications: {'peptide': 17}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 16}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.47, per 1000 atoms: 0.22
  Number of scatterers: 11460
  At special positions: 0
  Unit cell: (109.18, 107.12, 138.02, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      60     16.00
     P       6     15.00
     Mg      2     11.99
     O    2140      8.00
     N    1870      7.00
     C    7382      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 517.6 milliseconds
  

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2712

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 8 sheets defined
      61.3% alpha, 9.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 34
    Processing helix  chain 'A' and resid 38 through 47
    Processing helix  chain 'A' and resid 54 through 66
    Processing helix  chain 'A' and resid 124 through 132
    Processing helix  chain 'A' and resid 154 through 159
    Processing helix  chain 'A' and resid 160 through 163
    Processing helix  chain 'A' and resid 165 through 186
    Processing helix  chain 'A' and resid 188 through 196
    Processing helix  chain 'A' and resid 205 through 253
      removed outlier: 4.228A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 261
      removed outlier: 3.919A  pdb=" N   PHE A 258 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 269
      removed outlier: 3.551A  pdb=" N   ILE A 266 " --> pdb=" O   LYS A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 281
    Processing helix  chain 'A' and resid 281 through 305
      removed outlier: 3.599A  pdb=" N   LEU A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ILE A 287 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 354
      removed outlier: 3.654A  pdb=" N   ILE A 311 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   SER A 312 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   LYS A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      Proline residue:  A 329  - end of helix
      removed outlier: 4.079A  pdb=" N   GLN A 336 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 362
    Processing helix  chain 'A' and resid 363 through 417
    Processing helix  chain 'A' and resid 421 through 432
    Processing helix  chain 'A' and resid 435 through 460
      removed outlier: 3.605A  pdb=" N   VAL A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   GLN A 446 " --> pdb=" O   LEU A 442 " (cutoff:3.500A)
      Proline residue:  A 447  - end of helix
      removed outlier: 3.720A  pdb=" N   ARG A 458 " --> pdb=" O   VAL A 454 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LEU A 459 " --> pdb=" O   ALA A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 465
    Processing helix  chain 'A' and resid 525 through 533
      removed outlier: 4.043A  pdb=" N   ALA A 529 " --> pdb=" O   LYS A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 559
    Processing helix  chain 'A' and resid 575 through 581
    Processing helix  chain 'A' and resid 588 through 599
      removed outlier: 3.991A  pdb=" N   ILE A 592 " --> pdb=" O   ASP A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 606
    Processing helix  chain 'A' and resid 624 through 639
      removed outlier: 4.239A  pdb=" N   ARG A 630 " --> pdb=" O   GLY A 626 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU A 631 " --> pdb=" O   GLN A 627 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   ALA A 632 " --> pdb=" O   LYS A 628 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ILE A 633 " --> pdb=" O   GLN A 629 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   ALA A 634 " --> pdb=" O   ARG A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 667
    Processing helix  chain 'A' and resid 707 through 711
    Processing helix  chain 'A' and resid 712 through 722
      removed outlier: 3.634A  pdb=" N   GLU A 722 " --> pdb=" O   TRP A 718 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 21
      removed outlier: 3.556A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 34
    Processing helix  chain 'B' and resid 38 through 47
    Processing helix  chain 'B' and resid 54 through 66
    Processing helix  chain 'B' and resid 124 through 132
    Processing helix  chain 'B' and resid 153 through 159
      removed outlier: 3.644A  pdb=" N   LYS B 157 " --> pdb=" O   ASN B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 163
    Processing helix  chain 'B' and resid 165 through 186
    Processing helix  chain 'B' and resid 188 through 196
    Processing helix  chain 'B' and resid 205 through 253
      removed outlier: 4.248A  pdb=" N   PHE B 222 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 261
      removed outlier: 3.902A  pdb=" N   PHE B 258 " --> pdb=" O   PRO B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 269
      removed outlier: 3.549A  pdb=" N   ILE B 266 " --> pdb=" O   LYS B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 281
    Processing helix  chain 'B' and resid 281 through 305
      removed outlier: 3.748A  pdb=" N   LEU B 285 " --> pdb=" O   SER B 281 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ILE B 287 " --> pdb=" O   ALA B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 354
      removed outlier: 3.670A  pdb=" N   ILE B 311 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER B 312 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   LYS B 328 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
      Proline residue:  B 329  - end of helix
      removed outlier: 4.049A  pdb=" N   GLN B 336 " --> pdb=" O   ASN B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 362
    Processing helix  chain 'B' and resid 363 through 417
      removed outlier: 3.712A  pdb=" N   GLU B 368 " --> pdb=" O   GLU B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 432
    Processing helix  chain 'B' and resid 435 through 460
      removed outlier: 3.561A  pdb=" N   VAL B 439 " --> pdb=" O   PHE B 435 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLN B 446 " --> pdb=" O   LEU B 442 " (cutoff:3.500A)
      Proline residue:  B 447  - end of helix
      removed outlier: 3.612A  pdb=" N   ARG B 458 " --> pdb=" O   VAL B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 465
    Processing helix  chain 'B' and resid 524 through 533
      removed outlier: 3.846A  pdb=" N   ALA B 529 " --> pdb=" O   LYS B 525 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 553
      No H-bonds generated for 'chain 'B' and resid 551 through 553'
    Processing helix  chain 'B' and resid 554 through 561
    Processing helix  chain 'B' and resid 575 through 581
      removed outlier: 3.565A  pdb=" N   CYS B 581 " --> pdb=" O   LYS B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 588 through 600
      removed outlier: 3.737A  pdb=" N   ILE B 592 " --> pdb=" O   ASP B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 606
      removed outlier: 3.586A  pdb=" N   ILE B 605 " --> pdb=" O   ALA B 601 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 617 through 621
    Processing helix  chain 'B' and resid 624 through 639
      removed outlier: 3.638A  pdb=" N   ARG B 630 " --> pdb=" O   GLY B 626 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   LYS B 639 " --> pdb=" O   ARG B 635 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 654 through 669
      removed outlier: 4.030A  pdb=" N   GLU B 658 " --> pdb=" O   ASP B 654 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   GLU B 669 " --> pdb=" O   ILE B 665 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 681 through 685
      removed outlier: 3.536A  pdb=" N   ILE B 684 " --> pdb=" O   LEU B 681 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 703 through 710
    Processing helix  chain 'B' and resid 713 through 722
      removed outlier: 3.821A  pdb=" N   MET B 717 " --> pdb=" O   CYS B 713 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 21
      removed outlier: 3.609A  pdb=" N   MET D  21 " --> pdb=" O   GLU D  17 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 72
    Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 93
      removed outlier: 4.027A  pdb=" N   LEU A  97 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ILE A 103 " --> pdb=" O   ALA A 114 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   ALA A 114 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   SER A 105 " --> pdb=" O   THR A 112 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 509
      removed outlier: 4.072A  pdb=" N   LEU A 507 " --> pdb=" O   PHE A 488 " (cutoff:3.500A)
      removed outlier: 5.656A  pdb=" N   PHE A 488 " --> pdb=" O   LEU A 544 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   LEU A 544 " --> pdb=" O   PHE A 488 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   ASN A 490 " --> pdb=" O   ASP A 542 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   ASP A 542 " --> pdb=" O   ASN A 490 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   LYS A 540 " --> pdb=" O   ASP A 492 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 562 through 564
      removed outlier: 6.696A  pdb=" N   LEU A 644 " --> pdb=" O   ILE A 675 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   ILE A 677 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   LEU A 646 " --> pdb=" O   ILE A 677 " (cutoff:3.500A)
      removed outlier: 8.767A  pdb=" N   HIS A 679 " --> pdb=" O   LEU A 646 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   VAL A 515 " --> pdb=" O   VAL A 674 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLY A 519 " --> pdb=" O   ALA A 678 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   THR A 514 " --> pdb=" O   LYS A 689 " (cutoff:3.500A)
      removed outlier: 7.931A  pdb=" N   TYR A 691 " --> pdb=" O   THR A 514 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   ALA A 516 " --> pdb=" O   TYR A 691 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   LEU A 693 " --> pdb=" O   ALA A 516 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   VAL A 518 " --> pdb=" O   LEU A 693 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLU A 700 " --> pdb=" O   LEU A 692 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 36
    Processing sheet with id=AA6, first strand: chain 'B' and resid 67 through 72
      removed outlier: 4.035A  pdb=" N   LEU B  97 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   VAL B 102 " --> pdb=" O   ALA B 114 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 506 through 509
      removed outlier: 3.965A  pdb=" N   VAL B 491 " --> pdb=" O   LYS B 540 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   LYS B 540 " --> pdb=" O   VAL B 491 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 562 through 564
      removed outlier: 6.732A  pdb=" N   VAL B 515 " --> pdb=" O   ILE B 676 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ILE B 690 " --> pdb=" O   SER B 701 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   SER B 701 " --> pdb=" O   ILE B 690 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   LEU B 692 " --> pdb=" O   VAL B 699 " (cutoff:3.500A)

    678 hydrogen bonds defined for protein.
    1962 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: 2.22

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3576
        1.34 -     1.46: 1485
        1.46 -     1.57: 6460
        1.57 -     1.69: 11
        1.69 -     1.81: 104
  Bond restraints: 11636
  Sorted by residual:
  bond pdb=" N   MET A 533 "
       pdb=" CA  MET A 533 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.26e-02 6.30e+03 9.59e+00
  bond pdb=" N   VAL A 672 "
       pdb=" CA  VAL A 672 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.035 1.19e-02 7.06e+03 8.51e+00
  bond pdb=" N   VAL A 501 "
       pdb=" CA  VAL A 501 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.25e-02 6.40e+03 7.59e+00
  bond pdb=" N   LEU A 502 "
       pdb=" CA  LEU A 502 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.033 1.22e-02 6.72e+03 7.43e+00
  bond pdb=" N   ILE A 505 "
       pdb=" CA  ILE A 505 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.25e-02 6.40e+03 7.19e+00
  ... (remaining 11631 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 15333
        1.90 -     3.80: 312
        3.80 -     5.70: 36
        5.70 -     7.60: 9
        7.60 -     9.50: 6
  Bond angle restraints: 15696
  Sorted by residual:
  angle pdb=" N   GLU A 470 "
        pdb=" CA  GLU A 470 "
        pdb=" C   GLU A 470 "
      ideal   model   delta    sigma   weight residual
     111.28  120.78   -9.50 1.09e+00 8.42e-01 7.59e+01
  angle pdb=" N   LYS A 469 "
        pdb=" CA  LYS A 469 "
        pdb=" C   LYS A 469 "
      ideal   model   delta    sigma   weight residual
     111.28  120.68   -9.40 1.09e+00 8.42e-01 7.44e+01
  angle pdb=" N   GLU B 470 "
        pdb=" CA  GLU B 470 "
        pdb=" C   GLU B 470 "
      ideal   model   delta    sigma   weight residual
     111.28  119.74   -8.46 1.09e+00 8.42e-01 6.02e+01
  angle pdb=" N   LYS B 469 "
        pdb=" CA  LYS B 469 "
        pdb=" C   LYS B 469 "
      ideal   model   delta    sigma   weight residual
     111.28  119.01   -7.73 1.09e+00 8.42e-01 5.02e+01
  angle pdb=" N   GLU B 468 "
        pdb=" CA  GLU B 468 "
        pdb=" C   GLU B 468 "
      ideal   model   delta    sigma   weight residual
     111.28  117.62   -6.34 1.09e+00 8.42e-01 3.38e+01
  ... (remaining 15691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 6392
       17.66 -    35.32: 525
       35.32 -    52.97: 120
       52.97 -    70.63: 25
       70.63 -    88.29: 6
  Dihedral angle restraints: 7068
    sinusoidal: 2846
      harmonic: 4222
  Sorted by residual:
  dihedral pdb=" N   SER A 651 "
           pdb=" C   SER A 651 "
           pdb=" CA  SER A 651 "
           pdb=" CB  SER A 651 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.50   -8.70     0      2.50e+00 1.60e-01 1.21e+01
  dihedral pdb=" C   SER A 651 "
           pdb=" N   SER A 651 "
           pdb=" CA  SER A 651 "
           pdb=" CB  SER A 651 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.77    8.17     0      2.50e+00 1.60e-01 1.07e+01
  dihedral pdb=" CA  ASP A  94 "
           pdb=" CB  ASP A  94 "
           pdb=" CG  ASP A  94 "
           pdb=" OD1 ASP A  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.84   54.84     1      2.00e+01 2.50e-03 1.02e+01
  ... (remaining 7065 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1642
       0.068 -    0.136: 189
       0.136 -    0.204: 14
       0.204 -    0.271: 3
       0.271 -    0.339: 4
  Chirality restraints: 1852
  Sorted by residual:
  chirality pdb=" CA  LYS A 469 "
            pdb=" N   LYS A 469 "
            pdb=" C   LYS A 469 "
            pdb=" CB  LYS A 469 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.88e+00
  chirality pdb=" CA  SER A 651 "
            pdb=" N   SER A 651 "
            pdb=" C   SER A 651 "
            pdb=" CB  SER A 651 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.76e+00
  chirality pdb=" CA  GLU A 470 "
            pdb=" N   GLU A 470 "
            pdb=" C   GLU A 470 "
            pdb=" CB  GLU A 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.93e+00
  ... (remaining 1849 not shown)

  Planarity restraints: 1944
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 532 "   -0.028 2.00e-02 2.50e+03   5.52e-02 3.04e+01
        pdb=" C   LEU A 532 "    0.095 2.00e-02 2.50e+03
        pdb=" O   LEU A 532 "   -0.036 2.00e-02 2.50e+03
        pdb=" N   MET A 533 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 710 "    0.010 2.00e-02 2.50e+03   2.07e-02 4.30e+00
        pdb=" C   LEU A 710 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   LEU A 710 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LYS A 711 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 328 "   -0.029 5.00e-02 4.00e+02   4.39e-02 3.09e+00
        pdb=" N   PRO A 329 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 329 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 329 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1941 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.36: 13
        2.36 -     2.99: 6068
        2.99 -     3.63: 16922
        3.63 -     4.26: 24023
        4.26 -     4.90: 40984
  Nonbonded interactions: 88010
  Sorted by model distance:
  nonbonded pdb=" O2G ATP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     1.719 2.170
  nonbonded pdb=" OE1 GLN A 567 "
            pdb="MG    MG A 802 "
     model   vdw
     1.823 2.170
  nonbonded pdb=" O1B ATP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     1.824 2.170
  nonbonded pdb=" OD1 ASP B 647 "
            pdb=" N   GLU B 648 "
     model   vdw
     2.116 3.120
  nonbonded pdb=" N   GLU A 669 "
            pdb=" OE1 GLU A 669 "
     model   vdw
     2.197 3.120
  ... (remaining 88005 not shown)

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

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:             2.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.420
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
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      :  0.004   0.048  11636  Z= 0.199
  Angle     :  0.682   9.498  15696  Z= 0.433
  Chirality :  0.047   0.339   1852
  Planarity :  0.003   0.055   1944
  Dihedral  : 13.819  88.290   4356
  Min Nonbonded Distance : 1.719

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.30 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  0.64 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.22), residues: 1456
  helix:  1.42 (0.19), residues: 832
  sheet: -1.15 (0.42), residues: 138
  loop : -1.81 (0.24), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 458 
 TYR   0.013   0.001   TYR B 389 
 PHE   0.015   0.002   PHE A  83 
 TRP   0.028   0.002   TRP B 132 
 HIS   0.005   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (11636)
  covalent geometry    : angle       0.68227 (15696)
  hydrogen bonds       : bond        0.16305 (  678)
  hydrogen bonds       : angle       5.74859 ( 1962)

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

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

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  441 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 432
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 ASN cc_start: 0.8092 (m-40) cc_final: 0.7519 (t0)
REVERT: C   19 MET cc_start: 0.6545 (mmp) cc_final: 0.6144 (mmp)
REVERT: B   39 LEU cc_start: 0.8705 (tp) cc_final: 0.8442 (tp)
REVERT: B  518 VAL cc_start: 0.8792 (p) cc_final: 0.8563 (m)
REVERT: B  598 MET cc_start: 0.7849 (mtp) cc_final: 0.7547 (mtt)
  outliers start: 9
  outliers final: 1
  residues processed: 439
  average time/residue: 0.1039
  time to fit residues: 64.3262
Evaluate side-chains
  271 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 270
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
A  54 ASN
A  99 HIS
A 305 ASN
A 419 ASN
A 424 GLN
A 450 GLN
A 490 ASN
A 629 GLN
A 704 HIS
B  99 HIS
B 259 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.143280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.120097 restraints weight = 30832.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.123327 restraints weight = 14737.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.125374 restraints weight = 8912.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.126602 restraints weight = 6300.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.127565 restraints weight = 5027.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11636  Z= 0.167
  Angle     :  0.612   6.704  15696  Z= 0.322
  Chirality :  0.041   0.158   1852
  Planarity :  0.004   0.067   1944
  Dihedral  :  7.294  85.956   1622
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 15.65 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.22), residues: 1456
  helix:  1.79 (0.19), residues: 822
  sheet: -0.98 (0.42), residues: 142
  loop : -1.50 (0.25), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 261 
 TYR   0.013   0.001   TYR B 319 
 PHE   0.017   0.002   PHE B 217 
 TRP   0.014   0.002   TRP A 718 
 HIS   0.004   0.001   HIS A 704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (11636)
  covalent geometry    : angle       0.61154 (15696)
  hydrogen bonds       : bond        0.04883 (  678)
  hydrogen bonds       : angle       4.37834 ( 1962)

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

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

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 281
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 LEU cc_start: 0.9375 (tp) cc_final: 0.9152 (tt)
REVERT: A  305 ASN cc_start: 0.7498 (t0) cc_final: 0.7222 (t0)
REVERT: A  335 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7030 (ptp-110)
REVERT: A  606 GLU cc_start: 0.7633 (mp0) cc_final: 0.7346 (mp0)
REVERT: A  679 HIS cc_start: 0.7598 (t-90) cc_final: 0.7366 (p90)
REVERT: B   36 LYS cc_start: 0.8413 (ttmt) cc_final: 0.7988 (mtpp)
REVERT: B   49 ASP cc_start: 0.8513 (t0) cc_final: 0.8094 (p0)
REVERT: B   99 HIS cc_start: 0.8160 (t70) cc_final: 0.7900 (t70)
REVERT: B  239 ASP cc_start: 0.8882 (t0) cc_final: 0.8606 (t0)
REVERT: B  660 HIS cc_start: 0.8097 (t70) cc_final: 0.7807 (t70)
  outliers start: 43
  outliers final: 32
  residues processed: 308
  average time/residue: 0.0858
  time to fit residues: 39.4582
Evaluate side-chains
  276 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 243
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  335 ARG
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  566 SER
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain B residue  108 ASN
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  373 ASP
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  462 ILE
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  663 ASP
Chi-restraints excluded: chain B residue  679 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 97 optimal weight:    0.7980
   chunk 96 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 114 optimal weight:    0.0980
   chunk 22 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 68 optimal weight:    9.9990
   chunk 41 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 127 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
A  99 HIS
A 259 ASN
A 602 HIS
B 586 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.142607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.119203 restraints weight = 31264.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.122464 restraints weight = 14553.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.124524 restraints weight = 8679.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.125909 restraints weight = 6091.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.126707 restraints weight = 4825.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.3630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11636  Z= 0.136
  Angle     :  0.561   6.686  15696  Z= 0.293
  Chirality :  0.041   0.169   1852
  Planarity :  0.003   0.057   1944
  Dihedral  :  6.383  80.453   1622
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 19.74 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.22), residues: 1456
  helix:  1.88 (0.19), residues: 822
  sheet: -0.84 (0.42), residues: 140
  loop : -1.49 (0.25), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 335 
 TYR   0.009   0.001   TYR A 319 
 PHE   0.011   0.001   PHE B 257 
 TRP   0.013   0.001   TRP B 132 
 HIS   0.004   0.001   HIS A 704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (11636)
  covalent geometry    : angle       0.56131 (15696)
  hydrogen bonds       : bond        0.04475 (  678)
  hydrogen bonds       : angle       4.16582 ( 1962)

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

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

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 260
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 ASN cc_start: 0.7469 (t0) cc_final: 0.7220 (t0)
REVERT: A  340 ASP cc_start: 0.8790 (t0) cc_final: 0.8404 (t0)
REVERT: B   49 ASP cc_start: 0.8539 (t0) cc_final: 0.8195 (p0)
REVERT: B  637 LEU cc_start: 0.9281 (tp) cc_final: 0.8886 (pp)
REVERT: D   18 LEU cc_start: 0.9212 (mt) cc_final: 0.8888 (mm)
  outliers start: 48
  outliers final: 31
  residues processed: 288
  average time/residue: 0.0857
  time to fit residues: 36.8121
Evaluate side-chains
  268 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 237
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  566 SER
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain B residue  108 ASN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  356 GLU
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  663 ASP
Chi-restraints excluded: chain B residue  679 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 45 optimal weight:    0.3980
   chunk 58 optimal weight:   10.0000
   chunk 127 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 136 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
A  99 HIS
A 278 GLN
A 304 GLN
B  99 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.141372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.117959 restraints weight = 31340.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.121212 restraints weight = 14701.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.123249 restraints weight = 8805.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.124497 restraints weight = 6213.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.125462 restraints weight = 4956.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11636  Z= 0.139
  Angle     :  0.569   8.641  15696  Z= 0.293
  Chirality :  0.041   0.139   1852
  Planarity :  0.003   0.054   1944
  Dihedral  :  5.790  62.082   1622
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 20.30 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.22), residues: 1456
  helix:  1.92 (0.18), residues: 822
  sheet: -0.74 (0.42), residues: 140
  loop : -1.45 (0.25), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  96 
 TYR   0.013   0.001   TYR B 302 
 PHE   0.016   0.001   PHE A 213 
 TRP   0.011   0.001   TRP B 132 
 HIS   0.003   0.001   HIS A 704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (11636)
  covalent geometry    : angle       0.56949 (15696)
  hydrogen bonds       : bond        0.04363 (  678)
  hydrogen bonds       : angle       4.10211 ( 1962)

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

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

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 246
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 MET cc_start: 0.8137 (ttm) cc_final: 0.7864 (mtp)
REVERT: A  340 ASP cc_start: 0.8847 (t0) cc_final: 0.8437 (t0)
REVERT: C   17 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8519 (pt0)
REVERT: B  108 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7674 (p0)
REVERT: B  340 ASP cc_start: 0.8569 (t0) cc_final: 0.8253 (t0)
REVERT: B  637 LEU cc_start: 0.9284 (tp) cc_final: 0.9070 (pp)
REVERT: B  660 HIS cc_start: 0.8085 (t-170) cc_final: 0.7850 (t-170)
REVERT: D   18 LEU cc_start: 0.9169 (mt) cc_final: 0.8881 (mm)
  outliers start: 57
  outliers final: 40
  residues processed: 281
  average time/residue: 0.0818
  time to fit residues: 34.5951
Evaluate side-chains
  276 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 234
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  566 SER
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   99 HIS
Chi-restraints excluded: chain B residue  108 ASN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  350 GLU
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  356 GLU
Chi-restraints excluded: chain B residue  373 ASP
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  663 ASP
Chi-restraints excluded: chain B residue  679 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 126 optimal weight:    5.9990
   chunk 131 optimal weight:    3.9990
   chunk 132 optimal weight:    5.9990
   chunk 25 optimal weight:    0.3980
   chunk 89 optimal weight:    0.9980
   chunk 82 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
A  99 HIS
** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 GLN
B  99 HIS
** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 627 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.128873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.103932 restraints weight = 27722.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.106665 restraints weight = 14260.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.108498 restraints weight = 9039.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.109575 restraints weight = 6597.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.110330 restraints weight = 5407.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11636  Z= 0.169
  Angle     :  0.596   8.361  15696  Z= 0.308
  Chirality :  0.041   0.135   1852
  Planarity :  0.003   0.044   1944
  Dihedral  :  5.691  60.870   1622
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 22.31 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.22), residues: 1456
  helix:  1.84 (0.18), residues: 834
  sheet: -0.87 (0.42), residues: 140
  loop : -1.50 (0.25), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 269 
 TYR   0.010   0.001   TYR B 302 
 PHE   0.027   0.002   PHE B 715 
 TRP   0.009   0.001   TRP B 132 
 HIS   0.012   0.001   HIS B  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (11636)
  covalent geometry    : angle       0.59590 (15696)
  hydrogen bonds       : bond        0.04600 (  678)
  hydrogen bonds       : angle       4.18797 ( 1962)

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

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

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 244
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.8672 (mmt-90) cc_final: 0.8394 (mmt-90)
REVERT: A   41 LYS cc_start: 0.8992 (mmtm) cc_final: 0.8767 (mmmt)
REVERT: A  293 MET cc_start: 0.8202 (ttm) cc_final: 0.7846 (mtp)
REVERT: A  340 ASP cc_start: 0.8808 (t0) cc_final: 0.8420 (t0)
REVERT: A  450 GLN cc_start: 0.8762 (tp40) cc_final: 0.8328 (tp40)
REVERT: B  108 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7818 (p0)
REVERT: B  340 ASP cc_start: 0.8652 (t0) cc_final: 0.8281 (t0)
REVERT: B  660 HIS cc_start: 0.8348 (t-170) cc_final: 0.8106 (t-170)
REVERT: D   18 LEU cc_start: 0.9153 (mt) cc_final: 0.8887 (mm)
  outliers start: 60
  outliers final: 45
  residues processed: 279
  average time/residue: 0.0860
  time to fit residues: 35.6593
Evaluate side-chains
  279 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 233
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  566 SER
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   99 HIS
Chi-restraints excluded: chain B residue  108 ASN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  350 GLU
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  356 GLU
Chi-restraints excluded: chain B residue  373 ASP
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  663 ASP
Chi-restraints excluded: chain B residue  679 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 53 optimal weight:    0.5980
   chunk 117 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 70 optimal weight:    9.9990
   chunk 41 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 64 optimal weight:    9.9990
   chunk 142 optimal weight:    0.5980
   chunk 50 optimal weight:    0.1980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  99 HIS
A 278 GLN
** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 504 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 = 0.3902 r_free = 0.3902 target = 0.133097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.108910 restraints weight = 27548.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.111744 restraints weight = 13813.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.113598 restraints weight = 8574.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.114734 restraints weight = 6193.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.115579 restraints weight = 5001.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.4590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11636  Z= 0.118
  Angle     :  0.567   9.433  15696  Z= 0.290
  Chirality :  0.041   0.142   1852
  Planarity :  0.003   0.040   1944
  Dihedral  :  5.383  59.223   1622
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 23.52 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.22), residues: 1456
  helix:  1.93 (0.18), residues: 836
  sheet: -0.69 (0.42), residues: 138
  loop : -1.49 (0.25), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  96 
 TYR   0.009   0.001   TYR A 225 
 PHE   0.014   0.001   PHE B 428 
 TRP   0.012   0.001   TRP B 132 
 HIS   0.009   0.001   HIS B  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (11636)
  covalent geometry    : angle       0.56723 (15696)
  hydrogen bonds       : bond        0.04098 (  678)
  hydrogen bonds       : angle       3.98684 ( 1962)

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

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

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 256
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.8689 (mmt-90) cc_final: 0.8469 (mmt-90)
REVERT: A   41 LYS cc_start: 0.8975 (mmtm) cc_final: 0.8747 (mmmt)
REVERT: A  340 ASP cc_start: 0.8772 (t0) cc_final: 0.8370 (t0)
REVERT: A  450 GLN cc_start: 0.8730 (tp40) cc_final: 0.8354 (tp40)
REVERT: C   17 GLU cc_start: 0.8836 (pt0) cc_final: 0.8110 (pm20)
REVERT: B  108 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7942 (p0)
REVERT: B  189 TYR cc_start: 0.8994 (t80) cc_final: 0.8785 (t80)
REVERT: B  340 ASP cc_start: 0.8662 (t0) cc_final: 0.8220 (t0)
REVERT: B  660 HIS cc_start: 0.8298 (t-170) cc_final: 0.8061 (t-170)
REVERT: D   18 LEU cc_start: 0.9116 (mt) cc_final: 0.8869 (mm)
  outliers start: 43
  outliers final: 32
  residues processed: 281
  average time/residue: 0.0840
  time to fit residues: 35.4270
Evaluate side-chains
  272 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 239
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  566 SER
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue  108 ASN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  350 GLU
Chi-restraints excluded: chain B residue  356 GLU
Chi-restraints excluded: chain B residue  373 ASP
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  663 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0870
   chunk 66 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A  99 HIS
A 278 GLN
** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 ASN
B  99 HIS
B 249 HIS
B 278 GLN
** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.133122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.108850 restraints weight = 27451.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.111645 restraints weight = 13710.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.113574 restraints weight = 8541.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.114690 restraints weight = 6154.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.115473 restraints weight = 4989.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.4790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11636  Z= 0.121
  Angle     :  0.592   9.161  15696  Z= 0.301
  Chirality :  0.041   0.187   1852
  Planarity :  0.003   0.038   1944
  Dihedral  :  5.301  58.624   1622
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 23.92 %
    Favored  : 72.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.22), residues: 1456
  helix:  1.95 (0.18), residues: 836
  sheet: -0.63 (0.42), residues: 138
  loop : -1.44 (0.25), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 335 
 TYR   0.009   0.001   TYR A 225 
 PHE   0.034   0.001   PHE B 715 
 TRP   0.011   0.001   TRP B 132 
 HIS   0.003   0.001   HIS B 679 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (11636)
  covalent geometry    : angle       0.59235 (15696)
  hydrogen bonds       : bond        0.04051 (  678)
  hydrogen bonds       : angle       3.97046 ( 1962)

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

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

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 248
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.8648 (mmt-90) cc_final: 0.8440 (mmt-90)
REVERT: A   39 LEU cc_start: 0.9075 (mt) cc_final: 0.8811 (tp)
REVERT: A   41 LYS cc_start: 0.8925 (mmtm) cc_final: 0.8410 (mmmt)
REVERT: A  340 ASP cc_start: 0.8804 (t0) cc_final: 0.8426 (t0)
REVERT: A  450 GLN cc_start: 0.8737 (tp40) cc_final: 0.8289 (tp40)
REVERT: C   17 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8557 (pt0)
REVERT: B  108 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7867 (p0)
REVERT: B  340 ASP cc_start: 0.8641 (t0) cc_final: 0.8187 (t0)
REVERT: B  660 HIS cc_start: 0.8335 (t-170) cc_final: 0.8066 (t-170)
REVERT: D   18 LEU cc_start: 0.9128 (mt) cc_final: 0.8900 (mm)
  outliers start: 48
  outliers final: 36
  residues processed: 272
  average time/residue: 0.0856
  time to fit residues: 34.5555
Evaluate side-chains
  274 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 236
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  566 SER
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain A residue  644 LEU
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   99 HIS
Chi-restraints excluded: chain B residue  108 ASN
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  350 GLU
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  356 GLU
Chi-restraints excluded: chain B residue  373 ASP
Chi-restraints excluded: chain B residue  398 ILE
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  663 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 56 optimal weight:    0.4980
   chunk 65 optimal weight:    9.9990
   chunk 79 optimal weight:    3.9990
   chunk 69 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 1 optimal weight:    7.9990
   chunk 107 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
A  99 HIS
** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 HIS
** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.129784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.104997 restraints weight = 27682.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.107741 restraints weight = 14277.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.109574 restraints weight = 9070.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.110653 restraints weight = 6661.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.111423 restraints weight = 5468.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.4957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11636  Z= 0.168
  Angle     :  0.630   8.834  15696  Z= 0.322
  Chirality :  0.042   0.219   1852
  Planarity :  0.003   0.036   1944
  Dihedral  :  5.357  59.634   1622
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 24.64 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.22), residues: 1456
  helix:  1.91 (0.18), residues: 836
  sheet: -0.68 (0.42), residues: 138
  loop : -1.48 (0.25), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 277 
 TYR   0.011   0.001   TYR A 225 
 PHE   0.021   0.002   PHE A 428 
 TRP   0.008   0.001   TRP B 132 
 HIS   0.005   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (11636)
  covalent geometry    : angle       0.63023 (15696)
  hydrogen bonds       : bond        0.04500 (  678)
  hydrogen bonds       : angle       4.19855 ( 1962)

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

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

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 241
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 LYS cc_start: 0.8915 (mmtm) cc_final: 0.8708 (mmmt)
REVERT: A  270 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.9041 (t80)
REVERT: A  340 ASP cc_start: 0.8701 (t0) cc_final: 0.8313 (t0)
REVERT: A  450 GLN cc_start: 0.8772 (tp40) cc_final: 0.8324 (tp40)
REVERT: A  655 SER cc_start: 0.8886 (m) cc_final: 0.8638 (p)
REVERT: A  679 HIS cc_start: 0.7876 (t-90) cc_final: 0.7559 (t-90)
REVERT: B   99 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.7661 (t70)
REVERT: B  108 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7879 (p0)
REVERT: B  316 ILE cc_start: 0.9538 (tp) cc_final: 0.9303 (tp)
REVERT: B  340 ASP cc_start: 0.8677 (t0) cc_final: 0.8235 (t0)
REVERT: B  660 HIS cc_start: 0.8414 (t-170) cc_final: 0.8169 (t-170)
REVERT: D   18 LEU cc_start: 0.9119 (mt) cc_final: 0.8886 (mm)
  outliers start: 49
  outliers final: 38
  residues processed: 267
  average time/residue: 0.0879
  time to fit residues: 34.4919
Evaluate side-chains
  269 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 228
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  389 TYR
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  566 SER
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain C residue   22 THR
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   99 HIS
Chi-restraints excluded: chain B residue  108 ASN
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  350 GLU
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  356 GLU
Chi-restraints excluded: chain B residue  373 ASP
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  398 ILE
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  663 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 70 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 118 optimal weight:    2.9990
   chunk 90 optimal weight:    0.6980
   chunk 14 optimal weight:    7.9990
   chunk 140 optimal weight:    0.9980
   chunk 105 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  99 HIS
A 305 ASN
** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 504 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 = 0.3869 r_free = 0.3869 target = 0.131914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.107355 restraints weight = 27452.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.110140 restraints weight = 14129.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.111938 restraints weight = 8945.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.113091 restraints weight = 6554.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.113918 restraints weight = 5324.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.5105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11636  Z= 0.136
  Angle     :  0.655  16.085  15696  Z= 0.327
  Chirality :  0.042   0.210   1852
  Planarity :  0.003   0.037   1944
  Dihedral  :  5.294  59.045   1622
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 25.36 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.22), residues: 1456
  helix:  1.92 (0.18), residues: 832
  sheet: -0.71 (0.42), residues: 138
  loop : -1.50 (0.25), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 335 
 TYR   0.012   0.001   TYR A 150 
 PHE   0.020   0.001   PHE A 428 
 TRP   0.011   0.001   TRP B 132 
 HIS   0.003   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (11636)
  covalent geometry    : angle       0.65533 (15696)
  hydrogen bonds       : bond        0.04314 (  678)
  hydrogen bonds       : angle       4.10645 ( 1962)

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

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

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 232
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8657 (mmmt)
REVERT: A  270 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.9084 (t80)
REVERT: A  340 ASP cc_start: 0.8803 (t0) cc_final: 0.8431 (t0)
REVERT: A  450 GLN cc_start: 0.8741 (tp40) cc_final: 0.8274 (tp40)
REVERT: A  655 SER cc_start: 0.8819 (m) cc_final: 0.8557 (p)
REVERT: A  679 HIS cc_start: 0.7817 (t-90) cc_final: 0.7559 (t-90)
REVERT: C   17 GLU cc_start: 0.8838 (pt0) cc_final: 0.8147 (pt0)
REVERT: B  108 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7867 (p0)
REVERT: B  153 ASN cc_start: 0.8092 (t0) cc_final: 0.7664 (t0)
REVERT: B  154 MET cc_start: 0.8424 (ttp) cc_final: 0.8111 (ttm)
REVERT: B  316 ILE cc_start: 0.9507 (tp) cc_final: 0.9290 (tp)
REVERT: B  340 ASP cc_start: 0.8672 (t0) cc_final: 0.8372 (t0)
REVERT: B  461 GLU cc_start: 0.8473 (tp30) cc_final: 0.8025 (tp30)
REVERT: B  660 HIS cc_start: 0.8433 (t-170) cc_final: 0.8169 (t-170)
REVERT: D   18 LEU cc_start: 0.9124 (mt) cc_final: 0.8904 (mm)
REVERT: D   19 MET cc_start: 0.8888 (mmm) cc_final: 0.8686 (mmm)
  outliers start: 39
  outliers final: 36
  residues processed: 257
  average time/residue: 0.0826
  time to fit residues: 32.2133
Evaluate side-chains
  260 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 222
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  389 TYR
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  566 SER
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue  108 ASN
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  350 GLU
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  356 GLU
Chi-restraints excluded: chain B residue  373 ASP
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  398 ILE
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  663 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 5 optimal weight:    0.1980
   chunk 69 optimal weight:    0.6980
   chunk 142 optimal weight:    0.0870
   chunk 137 optimal weight:    7.9990
   chunk 101 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0670
   chunk 108 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.3696

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
A  99 HIS
** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 HIS
** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.133020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.108719 restraints weight = 27793.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.111600 restraints weight = 14013.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.113504 restraints weight = 8731.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.114613 restraints weight = 6310.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.115507 restraints weight = 5137.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.5260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  11636  Z= 0.124
  Angle     :  0.671  15.388  15696  Z= 0.333
  Chirality :  0.042   0.195   1852
  Planarity :  0.003   0.037   1944
  Dihedral  :  5.216  58.007   1622
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 26.00 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.22), residues: 1456
  helix:  1.98 (0.18), residues: 836
  sheet: -0.67 (0.42), residues: 138
  loop : -1.47 (0.25), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 335 
 TYR   0.010   0.001   TYR A 225 
 PHE   0.020   0.001   PHE A 428 
 TRP   0.011   0.001   TRP B 132 
 HIS   0.003   0.001   HIS B 679 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (11636)
  covalent geometry    : angle       0.67118 (15696)
  hydrogen bonds       : bond        0.03998 (  678)
  hydrogen bonds       : angle       4.05329 ( 1962)

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

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

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2912 Ramachandran restraints generated.
    1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 238
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8625 (mmmt)
REVERT: A  270 PHE cc_start: 0.9353 (OUTLIER) cc_final: 0.9083 (t80)
REVERT: A  340 ASP cc_start: 0.8745 (t0) cc_final: 0.8386 (t0)
REVERT: A  387 MET cc_start: 0.8236 (tpp) cc_final: 0.7890 (tpp)
REVERT: A  450 GLN cc_start: 0.8720 (tp40) cc_final: 0.8320 (tp40)
REVERT: A  655 SER cc_start: 0.8820 (m) cc_final: 0.8553 (p)
REVERT: A  679 HIS cc_start: 0.7789 (t-90) cc_final: 0.7557 (t-90)
REVERT: B   99 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7826 (t70)
REVERT: B  108 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7826 (p0)
REVERT: B  153 ASN cc_start: 0.8074 (t0) cc_final: 0.7428 (t0)
REVERT: B  154 MET cc_start: 0.8333 (ttp) cc_final: 0.8074 (ttm)
REVERT: B  340 ASP cc_start: 0.8610 (t0) cc_final: 0.8136 (t0)
REVERT: B  461 GLU cc_start: 0.8423 (tp30) cc_final: 0.7992 (tp30)
REVERT: B  660 HIS cc_start: 0.8375 (t-170) cc_final: 0.8130 (t-170)
REVERT: D   18 LEU cc_start: 0.9107 (mt) cc_final: 0.8899 (mm)
  outliers start: 31
  outliers final: 27
  residues processed: 254
  average time/residue: 0.0815
  time to fit residues: 31.5039
Evaluate side-chains
  262 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 232
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  389 TYR
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  618 GLU
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain C residue   22 THR
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   99 HIS
Chi-restraints excluded: chain B residue  108 ASN
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  350 GLU
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  356 GLU
Chi-restraints excluded: chain B residue  373 ASP
Chi-restraints excluded: chain B residue  398 ILE
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  663 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 103 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 120 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9980
   chunk 72 optimal weight:    7.9990
   chunk 7 optimal weight:    6.9990
   chunk 134 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 137 optimal weight:    2.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A  99 HIS
** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 HIS
** B 504 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 = 0.3871 r_free = 0.3871 target = 0.130597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.106149 restraints weight = 27915.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.108953 restraints weight = 14288.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.110793 restraints weight = 9011.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.112021 restraints weight = 6569.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.112834 restraints weight = 5316.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.5308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11636  Z= 0.153
  Angle     :  0.690  15.795  15696  Z= 0.342
  Chirality :  0.042   0.194   1852
  Planarity :  0.003   0.035   1944
  Dihedral  :  5.235  58.315   1622
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 26.40 %
    Favored  : 70.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.22), residues: 1456
  helix:  1.94 (0.18), residues: 836
  sheet: -0.73 (0.40), residues: 158
  loop : -1.55 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 335 
 TYR   0.010   0.001   TYR A 225 
 PHE   0.019   0.002   PHE A 428 
 TRP   0.009   0.001   TRP B 132 
 HIS   0.011   0.001   HIS B  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (11636)
  covalent geometry    : angle       0.69029 (15696)
  hydrogen bonds       : bond        0.04373 (  678)
  hydrogen bonds       : angle       4.21938 ( 1962)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1895.71 seconds
wall clock time: 33 minutes 35.88 seconds (2015.88 seconds total)