Starting phenix.real_space_refine
on Wed May 14 04:43:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qzc_18774/05_2025/8qzc_18774.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qzc_18774/05_2025/8qzc_18774.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qzc_18774/05_2025/8qzc_18774.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qzc_18774/05_2025/8qzc_18774.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qzc_18774/05_2025/8qzc_18774.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qzc_18774/05_2025/8qzc_18774.cif"
  }
  resolution = 3.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     S      72      5.16       5
     C    7472      2.51       5
     N    1888      2.21       5
     O    2032      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11468
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 701, 5732
          Classifications: {'peptide': 701}
          Link IDs: {'PTRANS': 30, 'TRANS': 670}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 5732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 701, 5732
          Classifications: {'peptide': 701}
          Link IDs: {'PTRANS': 30, 'TRANS': 670}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 7.30, per 1000 atoms: 0.64
  Number of scatterers: 11468
  At special positions: 0
  Unit cell: (90.283, 121.915, 113.348, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      4     19.99
     S      72     16.00
     O    2032      8.00
     N    1888      7.00
     C    7472      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 370 " - pdb=" SG  CYS A 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 836 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 386 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 625 " - pdb=" SG  CYS A 630 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 370 " - pdb=" SG  CYS B 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 836 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 382 " - pdb=" SG  CYS B 386 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 625 " - pdb=" SG  CYS B 630 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.40
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2688

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 10 sheets defined
      67.4% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 180
      removed outlier: 4.041A  pdb=" N   MET A 176 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      Proline residue:  A 177  - end of helix
    Processing helix  chain 'A' and resid 204 through 213
      removed outlier: 3.643A  pdb=" N   LYS A 208 " --> pdb=" O   PRO A 204 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   HIS A 212 " --> pdb=" O   LYS A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 226
      removed outlier: 3.648A  pdb=" N   SER A 225 " --> pdb=" O   TYR A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 241
      removed outlier: 3.672A  pdb=" N   PHE A 240 " --> pdb=" O   ARG A 237 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   PHE A 241 " --> pdb=" O   ASP A 238 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 237 through 241'
    Processing helix  chain 'A' and resid 242 through 257
    Processing helix  chain 'A' and resid 268 through 275
    Processing helix  chain 'A' and resid 296 through 305
    Processing helix  chain 'A' and resid 307 through 311
      removed outlier: 3.650A  pdb=" N   VAL A 310 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   PHE A 311 " --> pdb=" O   TYR A 308 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 307 through 311'
    Processing helix  chain 'A' and resid 316 through 358
      removed outlier: 7.524A  pdb=" N   GLU A 326 " --> pdb=" O   LYS A 322 " (cutoff:3.500A)
      removed outlier: 9.043A  pdb=" N   LYS A 327 " --> pdb=" O   TYR A 323 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   VAL A 328 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ILE A 343 " --> pdb=" O   THR A 339 " (cutoff:3.500A)
      Proline residue:  A 344  - end of helix
    Processing helix  chain 'A' and resid 359 through 362
    Processing helix  chain 'A' and resid 363 through 371
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'A' and resid 394 through 402
      removed outlier: 3.665A  pdb=" N   ALA A 398 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 405
      No H-bonds generated for 'chain 'A' and resid 403 through 405'
    Processing helix  chain 'A' and resid 406 through 439
      removed outlier: 3.531A  pdb=" N   VAL A 410 " --> pdb=" O   ASN A 406 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   MET A 432 " --> pdb=" O   LYS A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 465
    Processing helix  chain 'A' and resid 489 through 527
      removed outlier: 3.724A  pdb=" N   ALA A 519 " --> pdb=" O   ARG A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 569
      removed outlier: 4.070A  pdb=" N   GLU A 555 " --> pdb=" O   ILE A 551 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   VAL A 556 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLU A 568 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL A 569 " --> pdb=" O   THR A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 601
      Proline residue:  A 595  - end of helix
    Processing helix  chain 'A' and resid 617 through 619
      No H-bonds generated for 'chain 'A' and resid 617 through 619'
    Processing helix  chain 'A' and resid 630 through 651
      removed outlier: 3.937A  pdb=" N   LYS A 645 " --> pdb=" O   ILE A 641 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   GLN A 646 " --> pdb=" O   MET A 642 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLN A 649 " --> pdb=" O   LYS A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 693
      removed outlier: 3.728A  pdb=" N   VAL A 689 " --> pdb=" O   GLN A 685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 716
      removed outlier: 3.652A  pdb=" N   GLU A 705 " --> pdb=" O   PRO A 701 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   MET A 706 " --> pdb=" O   GLU A 702 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE A 716 " --> pdb=" O   PHE A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 744
      removed outlier: 3.938A  pdb=" N   VAL A 733 " --> pdb=" O   LEU A 729 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ARG A 736 " --> pdb=" O   ILE A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 782
      removed outlier: 3.933A  pdb=" N   ASN A 762 " --> pdb=" O   GLY A 758 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   VAL A 772 " --> pdb=" O   GLY A 768 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ILE A 773 " --> pdb=" O   LYS A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 795
    Processing helix  chain 'A' and resid 803 through 809
    Processing helix  chain 'A' and resid 815 through 817
      No H-bonds generated for 'chain 'A' and resid 815 through 817'
    Processing helix  chain 'A' and resid 854 through 886
      removed outlier: 3.783A  pdb=" N   TRP A 858 " --> pdb=" O   SER A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 910
      removed outlier: 3.906A  pdb=" N   ARG A 910 " --> pdb=" O   GLU A 906 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 181
      removed outlier: 4.011A  pdb=" N   MET B 176 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      Proline residue:  B 177  - end of helix
    Processing helix  chain 'B' and resid 202 through 204
      No H-bonds generated for 'chain 'B' and resid 202 through 204'
    Processing helix  chain 'B' and resid 205 through 213
      removed outlier: 3.847A  pdb=" N   HIS B 212 " --> pdb=" O   LYS B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 226
      removed outlier: 3.543A  pdb=" N   SER B 225 " --> pdb=" O   TYR B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 241
      removed outlier: 3.726A  pdb=" N   PHE B 240 " --> pdb=" O   ARG B 237 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   PHE B 241 " --> pdb=" O   ASP B 238 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 237 through 241'
    Processing helix  chain 'B' and resid 242 through 257
    Processing helix  chain 'B' and resid 268 through 275
    Processing helix  chain 'B' and resid 296 through 305
    Processing helix  chain 'B' and resid 307 through 311
      removed outlier: 3.631A  pdb=" N   VAL B 310 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   PHE B 311 " --> pdb=" O   TYR B 308 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 307 through 311'
    Processing helix  chain 'B' and resid 316 through 358
      removed outlier: 7.512A  pdb=" N   GLU B 326 " --> pdb=" O   LYS B 322 " (cutoff:3.500A)
      removed outlier: 9.017A  pdb=" N   LYS B 327 " --> pdb=" O   TYR B 323 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   VAL B 328 " --> pdb=" O   PHE B 324 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE B 343 " --> pdb=" O   THR B 339 " (cutoff:3.500A)
      Proline residue:  B 344  - end of helix
    Processing helix  chain 'B' and resid 359 through 362
    Processing helix  chain 'B' and resid 363 through 371
    Processing helix  chain 'B' and resid 391 through 393
      No H-bonds generated for 'chain 'B' and resid 391 through 393'
    Processing helix  chain 'B' and resid 394 through 402
      removed outlier: 3.662A  pdb=" N   ALA B 398 " --> pdb=" O   ALA B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 405
      No H-bonds generated for 'chain 'B' and resid 403 through 405'
    Processing helix  chain 'B' and resid 406 through 439
      removed outlier: 3.523A  pdb=" N   VAL B 410 " --> pdb=" O   ASN B 406 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   MET B 432 " --> pdb=" O   LYS B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 465
    Processing helix  chain 'B' and resid 489 through 527
      removed outlier: 3.715A  pdb=" N   ALA B 519 " --> pdb=" O   ARG B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 569
      removed outlier: 4.068A  pdb=" N   GLU B 555 " --> pdb=" O   ILE B 551 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   VAL B 556 " --> pdb=" O   LEU B 552 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLU B 568 " --> pdb=" O   LEU B 564 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL B 569 " --> pdb=" O   THR B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 601
      Proline residue:  B 595  - end of helix
    Processing helix  chain 'B' and resid 617 through 619
      No H-bonds generated for 'chain 'B' and resid 617 through 619'
    Processing helix  chain 'B' and resid 630 through 651
      removed outlier: 3.959A  pdb=" N   LYS B 645 " --> pdb=" O   ILE B 641 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   GLN B 646 " --> pdb=" O   MET B 642 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLN B 649 " --> pdb=" O   LYS B 645 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 685 through 693
      removed outlier: 3.701A  pdb=" N   VAL B 689 " --> pdb=" O   GLN B 685 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 699 through 716
      removed outlier: 3.655A  pdb=" N   GLU B 705 " --> pdb=" O   PRO B 701 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   MET B 706 " --> pdb=" O   GLU B 702 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE B 716 " --> pdb=" O   PHE B 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 722 through 744
      removed outlier: 3.921A  pdb=" N   VAL B 733 " --> pdb=" O   LEU B 729 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ARG B 736 " --> pdb=" O   ILE B 732 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 758 through 782
      removed outlier: 3.942A  pdb=" N   ASN B 762 " --> pdb=" O   GLY B 758 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   VAL B 772 " --> pdb=" O   GLY B 768 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   ILE B 773 " --> pdb=" O   LYS B 769 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 785 through 795
    Processing helix  chain 'B' and resid 803 through 809
    Processing helix  chain 'B' and resid 815 through 817
      No H-bonds generated for 'chain 'B' and resid 815 through 817'
    Processing helix  chain 'B' and resid 854 through 886
      removed outlier: 3.780A  pdb=" N   TRP B 858 " --> pdb=" O   SER B 854 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 890 through 910
      removed outlier: 3.893A  pdb=" N   ARG B 910 " --> pdb=" O   GLU B 906 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126
      removed outlier: 3.893A  pdb=" N   ALA A 279 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 190
      removed outlier: 3.525A  pdb=" N   THR A 187 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 218
    Processing sheet with id=AA4, first strand: chain 'A' and resid 615 through 616
    Processing sheet with id=AA5, first strand: chain 'A' and resid 810 through 813
    Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 126
      removed outlier: 3.939A  pdb=" N   ALA B 279 " --> pdb=" O   PHE B 126 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190
      removed outlier: 3.583A  pdb=" N   THR B 187 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 217 through 218
    Processing sheet with id=AA9, first strand: chain 'B' and resid 615 through 616
    Processing sheet with id=AB1, first strand: chain 'B' and resid 810 through 813

    661 hydrogen bonds defined for protein.
    1947 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: 3.57

  Time building geometry restraints manager: 2.86 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: 3562
        1.34 -     1.46: 2914
        1.46 -     1.58: 5160
        1.58 -     1.70: 0
        1.70 -     1.82: 118
  Bond restraints: 11754
  Sorted by residual:
  bond pdb=" CB  GLU A 555 "
       pdb=" CG  GLU A 555 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.14e+00
  bond pdb=" CB  GLU B 555 "
       pdb=" CG  GLU B 555 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 3.00e-02 1.11e+03 2.10e+00
  bond pdb=" SD  MET A 416 "
       pdb=" CE  MET A 416 "
    ideal  model  delta    sigma   weight residual
    1.791  1.755  0.036 2.50e-02 1.60e+03 2.02e+00
  bond pdb=" SD  MET B 416 "
       pdb=" CE  MET B 416 "
    ideal  model  delta    sigma   weight residual
    1.791  1.756  0.035 2.50e-02 1.60e+03 2.01e+00
  bond pdb=" CB  ASP B 883 "
       pdb=" CG  ASP B 883 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 2.50e-02 1.60e+03 1.75e+00
  ... (remaining 11749 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 15678
        2.68 -     5.37: 178
        5.37 -     8.05: 44
        8.05 -    10.74: 6
       10.74 -    13.42: 6
  Bond angle restraints: 15912
  Sorted by residual:
  angle pdb=" CB  MET A 424 "
        pdb=" CG  MET A 424 "
        pdb=" SD  MET A 424 "
      ideal   model   delta    sigma   weight residual
     112.70  124.93  -12.23 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" C   TYR B 288 "
        pdb=" N   GLU B 289 "
        pdb=" CA  GLU B 289 "
      ideal   model   delta    sigma   weight residual
     122.08  127.90   -5.82 1.47e+00 4.63e-01 1.56e+01
  angle pdb=" CB  MET B 424 "
        pdb=" CG  MET B 424 "
        pdb=" SD  MET B 424 "
      ideal   model   delta    sigma   weight residual
     112.70  124.42  -11.72 3.00e+00 1.11e-01 1.53e+01
  angle pdb=" C   TYR A 288 "
        pdb=" N   GLU A 289 "
        pdb=" CA  GLU A 289 "
      ideal   model   delta    sigma   weight residual
     122.08  127.81   -5.73 1.47e+00 4.63e-01 1.52e+01
  angle pdb=" CA  LEU B 191 "
        pdb=" CB  LEU B 191 "
        pdb=" CG  LEU B 191 "
      ideal   model   delta    sigma   weight residual
     116.30  129.72  -13.42 3.50e+00 8.16e-02 1.47e+01
  ... (remaining 15907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.03: 6166
       16.03 -    32.06: 702
       32.06 -    48.08: 127
       48.08 -    64.11: 21
       64.11 -    80.14: 6
  Dihedral angle restraints: 7022
    sinusoidal: 2870
      harmonic: 4152
  Sorted by residual:
  dihedral pdb=" CB  CYS B 382 "
           pdb=" SG  CYS B 382 "
           pdb=" SG  CYS B 386 "
           pdb=" CB  CYS B 386 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -149.60   63.60     1      1.00e+01 1.00e-02 5.33e+01
  dihedral pdb=" CB  CYS A 382 "
           pdb=" SG  CYS A 382 "
           pdb=" SG  CYS A 386 "
           pdb=" CB  CYS A 386 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -149.37   63.37     1      1.00e+01 1.00e-02 5.30e+01
  dihedral pdb=" CB  CYS B 625 "
           pdb=" SG  CYS B 625 "
           pdb=" SG  CYS B 630 "
           pdb=" CB  CYS B 630 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -46.12  -39.88     1      1.00e+01 1.00e-02 2.23e+01
  ... (remaining 7019 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1314
       0.051 -    0.102: 352
       0.102 -    0.154: 80
       0.154 -    0.205: 3
       0.205 -    0.256: 5
  Chirality restraints: 1754
  Sorted by residual:
  chirality pdb=" CA  GLU B 425 "
            pdb=" N   GLU B 425 "
            pdb=" C   GLU B 425 "
            pdb=" CB  GLU B 425 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CB  VAL A 569 "
            pdb=" CA  VAL A 569 "
            pdb=" CG1 VAL A 569 "
            pdb=" CG2 VAL A 569 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CB  VAL B 750 "
            pdb=" CA  VAL B 750 "
            pdb=" CG1 VAL B 750 "
            pdb=" CG2 VAL B 750 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 1751 not shown)

  Planarity restraints: 1998
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 176 "   -0.038 5.00e-02 4.00e+02   5.77e-02 5.32e+00
        pdb=" N   PRO A 177 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 177 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 177 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 176 "    0.037 5.00e-02 4.00e+02   5.52e-02 4.87e+00
        pdb=" N   PRO B 177 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B 177 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 177 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 406 "   -0.030 5.00e-02 4.00e+02   4.48e-02 3.21e+00
        pdb=" N   PRO B 407 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 407 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 407 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1995 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2328
        2.78 -     3.31: 10850
        3.31 -     3.84: 18851
        3.84 -     4.37: 21116
        4.37 -     4.90: 37307
  Nonbonded interactions: 90452
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 590 "
            pdb=" OG1 THR B 594 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   VAL A 590 "
            pdb=" OG1 THR A 594 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   LYS A 175 "
            pdb=" OG1 THR A 178 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG  SER A 387 "
            pdb=" OD2 ASP A 828 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG  SER B 387 "
            pdb=" OD2 ASP B 828 "
     model   vdw
     2.291 3.040
  ... (remaining 90447 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.800
  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:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     27.520
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.070
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
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   0.047  11762  Z= 0.187
  Angle     :  0.816  13.424  15928  Z= 0.421
  Chirality :  0.049   0.256   1754
  Planarity :  0.006   0.058   1998
  Dihedral  : 13.360  80.141   4310
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.20), residues: 1382
  helix: -0.05 (0.16), residues: 856
  sheet: -1.79 (0.99), residues: 28
  loop : -2.35 (0.24), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 427 
 HIS   0.004   0.001   HIS A 230 
 PHE   0.028   0.002   PHE B 324 
 TYR   0.026   0.002   TYR B 222 
 ARG   0.007   0.000   ARG B 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09950 (  661)
  hydrogen bonds       : angle       5.81106 ( 1947)
  SS BOND              : bond        0.00489 (    8)
  SS BOND              : angle       2.21171 (   16)
  covalent geometry    : bond        0.00389 (11754)
  covalent geometry    : angle       0.81325 (15912)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 1.202 
Fit side-chains
REVERT: A  827 LEU cc_start: 0.7498 (mt) cc_final: 0.7217 (mp)
REVERT: A  909 MET cc_start: 0.5081 (ttm) cc_final: 0.3630 (tpt)
REVERT: B  827 LEU cc_start: 0.7553 (mt) cc_final: 0.7310 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.2467
  time to fit residues: 60.2616
Evaluate side-chains
  130 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    0.9990
   chunk 106 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 109 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 127 optimal weight:    2.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.188321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.144282 restraints weight = 13899.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 1.88
r_work: 0.3595 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.1310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11762  Z= 0.179
  Angle     :  0.611   8.552  15928  Z= 0.318
  Chirality :  0.042   0.198   1754
  Planarity :  0.004   0.048   1998
  Dihedral  :  4.273  16.034   1546
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  7.69 %
    Favored  : 91.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.22), residues: 1382
  helix:  0.91 (0.17), residues: 854
  sheet: -2.84 (0.59), residues: 58
  loop : -2.02 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 427 
 HIS   0.008   0.001   HIS B 402 
 PHE   0.018   0.002   PHE A 126 
 TYR   0.015   0.002   TYR B 838 
 ARG   0.004   0.000   ARG B 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04204 (  661)
  hydrogen bonds       : angle       4.22435 ( 1947)
  SS BOND              : bond        0.00323 (    8)
  SS BOND              : angle       1.95773 (   16)
  covalent geometry    : bond        0.00425 (11754)
  covalent geometry    : angle       0.60863 (15912)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 148
  time to evaluate  : 1.349 
Fit side-chains
REVERT: A  215 GLN cc_start: 0.7388 (pp30) cc_final: 0.6409 (pp30)
REVERT: A  691 PHE cc_start: 0.8419 (t80) cc_final: 0.8215 (t80)
REVERT: A  752 ILE cc_start: 0.8232 (tt) cc_final: 0.7593 (mm)
REVERT: B  215 GLN cc_start: 0.7491 (pp30) cc_final: 0.7236 (pt0)
REVERT: B  752 ILE cc_start: 0.8219 (tt) cc_final: 0.7582 (mm)
  outliers start: 9
  outliers final: 7
  residues processed: 152
  average time/residue: 0.2354
  time to fit residues: 51.9428
Evaluate side-chains
  139 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 132
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  733 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 105 optimal weight:    8.9990
   chunk 56 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 111 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 108 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   chunk 128 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 69 optimal weight:   10.0000
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.186533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.143403 restraints weight = 13968.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 1.91
r_work: 0.3567 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11762  Z= 0.177
  Angle     :  0.607   8.000  15928  Z= 0.315
  Chirality :  0.043   0.191   1754
  Planarity :  0.004   0.044   1998
  Dihedral  :  4.223  15.184   1546
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  9.94 %
    Favored  : 88.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.22), residues: 1382
  helix:  1.15 (0.17), residues: 854
  sheet: -3.07 (0.58), residues: 58
  loop : -2.01 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 427 
 HIS   0.005   0.001   HIS A 402 
 PHE   0.028   0.002   PHE A 126 
 TYR   0.015   0.002   TYR A 838 
 ARG   0.002   0.000   ARG A 753 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04143 (  661)
  hydrogen bonds       : angle       4.10940 ( 1947)
  SS BOND              : bond        0.00266 (    8)
  SS BOND              : angle       1.57889 (   16)
  covalent geometry    : bond        0.00424 (11754)
  covalent geometry    : angle       0.60484 (15912)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 1.372 
Fit side-chains
REVERT: A  215 GLN cc_start: 0.7308 (pp30) cc_final: 0.6345 (pp30)
REVERT: A  752 ILE cc_start: 0.8272 (tt) cc_final: 0.7664 (mm)
REVERT: B  215 GLN cc_start: 0.7470 (pp30) cc_final: 0.7247 (pt0)
REVERT: B  752 ILE cc_start: 0.8198 (tt) cc_final: 0.7542 (mm)
  outliers start: 16
  outliers final: 10
  residues processed: 147
  average time/residue: 0.2444
  time to fit residues: 52.0846
Evaluate side-chains
  141 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  733 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 78 optimal weight:    0.0030
   chunk 14 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9980
   chunk 105 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9980
   chunk 23 optimal weight:    0.2980
   chunk 2 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 96 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.196147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.156947 restraints weight = 14168.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3955 rms_B_bonded: 1.79
r_work: 0.3729 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3603 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  11762  Z= 0.114
  Angle     :  0.555   7.822  15928  Z= 0.284
  Chirality :  0.040   0.195   1754
  Planarity :  0.003   0.043   1998
  Dihedral  :  4.113  22.449   1546
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 11.38 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.22), residues: 1382
  helix:  1.50 (0.17), residues: 854
  sheet: -3.12 (0.57), residues: 58
  loop : -1.93 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 427 
 HIS   0.004   0.001   HIS B 402 
 PHE   0.028   0.001   PHE A 126 
 TYR   0.010   0.001   TYR B 838 
 ARG   0.002   0.000   ARG B 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03620 (  661)
  hydrogen bonds       : angle       3.90105 ( 1947)
  SS BOND              : bond        0.00282 (    8)
  SS BOND              : angle       2.01940 (   16)
  covalent geometry    : bond        0.00248 (11754)
  covalent geometry    : angle       0.55119 (15912)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 142
  time to evaluate  : 1.405 
Fit side-chains
REVERT: A  215 GLN cc_start: 0.7258 (pp30) cc_final: 0.6938 (pt0)
REVERT: A  691 PHE cc_start: 0.8471 (t80) cc_final: 0.8184 (t80)
REVERT: A  706 MET cc_start: 0.8562 (mmp) cc_final: 0.8300 (mmp)
REVERT: A  752 ILE cc_start: 0.8357 (tt) cc_final: 0.7801 (mm)
REVERT: A  909 MET cc_start: 0.4862 (ttm) cc_final: 0.3570 (tpt)
REVERT: B  215 GLN cc_start: 0.7538 (pp30) cc_final: 0.7253 (pt0)
REVERT: B  706 MET cc_start: 0.8542 (mmp) cc_final: 0.8283 (mmp)
REVERT: B  752 ILE cc_start: 0.8265 (tt) cc_final: 0.7682 (mm)
  outliers start: 7
  outliers final: 3
  residues processed: 147
  average time/residue: 0.2337
  time to fit residues: 49.7463
Evaluate side-chains
  135 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 132
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  757 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 116 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 56 optimal weight:    0.5980
   chunk 76 optimal weight:    8.9990
   chunk 118 optimal weight:    0.6980
   chunk 128 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 114 optimal weight:    5.9990
   chunk 135 optimal weight:    1.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.192503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.154501 restraints weight = 14166.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3926 rms_B_bonded: 1.99
r_work: 0.3663 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3536 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11762  Z= 0.170
  Angle     :  0.599   8.135  15928  Z= 0.309
  Chirality :  0.042   0.169   1754
  Planarity :  0.004   0.042   1998
  Dihedral  :  4.193  20.736   1546
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 12.34 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.22), residues: 1382
  helix:  1.43 (0.17), residues: 854
  sheet: -3.23 (0.59), residues: 58
  loop : -1.93 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 427 
 HIS   0.005   0.001   HIS A 402 
 PHE   0.026   0.002   PHE A 126 
 TYR   0.015   0.002   TYR A 838 
 ARG   0.003   0.000   ARG A 748 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04077 (  661)
  hydrogen bonds       : angle       4.00202 ( 1947)
  SS BOND              : bond        0.00224 (    8)
  SS BOND              : angle       2.27612 (   16)
  covalent geometry    : bond        0.00408 (11754)
  covalent geometry    : angle       0.59451 (15912)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 142
  time to evaluate  : 1.342 
Fit side-chains
REVERT: A  126 PHE cc_start: 0.6838 (t80) cc_final: 0.6594 (t80)
REVERT: A  215 GLN cc_start: 0.7272 (pp30) cc_final: 0.6979 (pt0)
REVERT: A  691 PHE cc_start: 0.8469 (t80) cc_final: 0.8212 (t80)
REVERT: A  706 MET cc_start: 0.8745 (mmp) cc_final: 0.8493 (mmp)
REVERT: A  752 ILE cc_start: 0.8383 (tt) cc_final: 0.7796 (mm)
REVERT: B  706 MET cc_start: 0.8741 (mmp) cc_final: 0.8498 (mmp)
REVERT: B  752 ILE cc_start: 0.8326 (tt) cc_final: 0.7724 (mm)
  outliers start: 21
  outliers final: 17
  residues processed: 156
  average time/residue: 0.2291
  time to fit residues: 51.4734
Evaluate side-chains
  148 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  369 MET
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  690 ASP
Chi-restraints excluded: chain B residue  757 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 77 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 88 optimal weight:    0.5980
   chunk 4 optimal weight:    6.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.194277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.155135 restraints weight = 14280.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 1.94
r_work: 0.3697 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3563 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11762  Z= 0.126
  Angle     :  0.566   8.496  15928  Z= 0.290
  Chirality :  0.040   0.210   1754
  Planarity :  0.003   0.042   1998
  Dihedral  :  4.066  18.386   1546
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.90 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.22), residues: 1382
  helix:  1.62 (0.18), residues: 854
  sheet: -3.26 (0.59), residues: 58
  loop : -1.91 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 427 
 HIS   0.005   0.001   HIS A 402 
 PHE   0.023   0.001   PHE A 126 
 TYR   0.011   0.001   TYR A 838 
 ARG   0.002   0.000   ARG B 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03756 (  661)
  hydrogen bonds       : angle       3.93064 ( 1947)
  SS BOND              : bond        0.00242 (    8)
  SS BOND              : angle       1.91387 (   16)
  covalent geometry    : bond        0.00288 (11754)
  covalent geometry    : angle       0.56324 (15912)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 1.184 
Fit side-chains
REVERT: A  215 GLN cc_start: 0.7204 (pp30) cc_final: 0.6934 (pt0)
REVERT: A  691 PHE cc_start: 0.8448 (t80) cc_final: 0.8137 (t80)
REVERT: A  752 ILE cc_start: 0.8349 (tt) cc_final: 0.7767 (mm)
REVERT: B  752 ILE cc_start: 0.8286 (tt) cc_final: 0.7682 (mm)
  outliers start: 20
  outliers final: 18
  residues processed: 153
  average time/residue: 0.2286
  time to fit residues: 50.5919
Evaluate side-chains
  145 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 1.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  690 ASP
Chi-restraints excluded: chain B residue  717 VAL
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 108 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 23 optimal weight:    0.1980
   chunk 54 optimal weight:    0.8980
   chunk 121 optimal weight:    1.9990
   chunk 130 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9980
   chunk 71 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.194907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.156226 restraints weight = 14287.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 1.93
r_work: 0.3699 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3574 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11762  Z= 0.125
  Angle     :  0.558   8.730  15928  Z= 0.285
  Chirality :  0.040   0.205   1754
  Planarity :  0.003   0.042   1998
  Dihedral  :  4.017  17.295   1546
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 13.62 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.23), residues: 1382
  helix:  1.68 (0.18), residues: 854
  sheet: -3.29 (0.59), residues: 58
  loop : -1.88 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 427 
 HIS   0.004   0.001   HIS B 402 
 PHE   0.020   0.001   PHE B 126 
 TYR   0.010   0.001   TYR A 687 
 ARG   0.003   0.000   ARG A 788 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03707 (  661)
  hydrogen bonds       : angle       3.88143 ( 1947)
  SS BOND              : bond        0.00252 (    8)
  SS BOND              : angle       1.78508 (   16)
  covalent geometry    : bond        0.00284 (11754)
  covalent geometry    : angle       0.55573 (15912)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 1.192 
Fit side-chains
REVERT: A  215 GLN cc_start: 0.7178 (pp30) cc_final: 0.6932 (pt0)
REVERT: A  691 PHE cc_start: 0.8405 (t80) cc_final: 0.8138 (t80)
REVERT: A  909 MET cc_start: 0.4847 (ttm) cc_final: 0.3613 (tpt)
REVERT: B  752 ILE cc_start: 0.8277 (tt) cc_final: 0.7676 (mm)
  outliers start: 20
  outliers final: 16
  residues processed: 146
  average time/residue: 0.2184
  time to fit residues: 46.6781
Evaluate side-chains
  144 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  690 ASP
Chi-restraints excluded: chain B residue  717 VAL
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 114 optimal weight:    0.9980
   chunk 136 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 132 optimal weight:    0.5980
   chunk 134 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.194418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.155155 restraints weight = 14301.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 1.90
r_work: 0.3700 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3572 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11762  Z= 0.133
  Angle     :  0.571   8.961  15928  Z= 0.291
  Chirality :  0.040   0.193   1754
  Planarity :  0.003   0.031   1998
  Dihedral  :  4.028  16.605   1546
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.18 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.23), residues: 1382
  helix:  1.68 (0.18), residues: 854
  sheet: -3.30 (0.60), residues: 58
  loop : -1.85 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 427 
 HIS   0.005   0.001   HIS B 402 
 PHE   0.018   0.001   PHE B 126 
 TYR   0.011   0.001   TYR A 838 
 ARG   0.004   0.000   ARG B 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03741 (  661)
  hydrogen bonds       : angle       3.90873 ( 1947)
  SS BOND              : bond        0.00244 (    8)
  SS BOND              : angle       1.83888 (   16)
  covalent geometry    : bond        0.00307 (11754)
  covalent geometry    : angle       0.56847 (15912)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 1.158 
Fit side-chains
REVERT: A  215 GLN cc_start: 0.7220 (pp30) cc_final: 0.6988 (pt0)
REVERT: A  691 PHE cc_start: 0.8426 (t80) cc_final: 0.8173 (t80)
REVERT: A  909 MET cc_start: 0.4914 (ttm) cc_final: 0.3714 (tpt)
REVERT: B  752 ILE cc_start: 0.8312 (tt) cc_final: 0.7693 (mm)
  outliers start: 20
  outliers final: 19
  residues processed: 148
  average time/residue: 0.2335
  time to fit residues: 50.6094
Evaluate side-chains
  147 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 1.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  690 ASP
Chi-restraints excluded: chain B residue  717 VAL
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 84 optimal weight:    0.3980
   chunk 2 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 39 optimal weight:   10.0000
   chunk 33 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 104 optimal weight:   10.0000
   chunk 93 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 692 ASN
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.189540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.151384 restraints weight = 14358.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 1.98
r_work: 0.3632 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3506 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.2320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  11762  Z= 0.218
  Angle     :  0.653   9.319  15928  Z= 0.339
  Chirality :  0.044   0.180   1754
  Planarity :  0.004   0.032   1998
  Dihedral  :  4.330  18.397   1546
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.66 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.22), residues: 1382
  helix:  1.34 (0.17), residues: 852
  sheet: -3.51 (0.58), residues: 60
  loop : -1.91 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 427 
 HIS   0.005   0.001   HIS B 402 
 PHE   0.017   0.002   PHE B 126 
 TYR   0.018   0.002   TYR A 838 
 ARG   0.003   0.000   ARG B 748 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04376 (  661)
  hydrogen bonds       : angle       4.16397 ( 1947)
  SS BOND              : bond        0.00214 (    8)
  SS BOND              : angle       2.05438 (   16)
  covalent geometry    : bond        0.00536 (11754)
  covalent geometry    : angle       0.64986 (15912)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 1.300 
Fit side-chains
REVERT: A  176 MET cc_start: 0.6024 (ttt) cc_final: 0.5675 (ttt)
REVERT: A  215 GLN cc_start: 0.7185 (pp30) cc_final: 0.6953 (pt0)
REVERT: A  691 PHE cc_start: 0.8418 (t80) cc_final: 0.8197 (t80)
REVERT: A  752 ILE cc_start: 0.8469 (tt) cc_final: 0.7877 (mm)
REVERT: B  254 LEU cc_start: 0.8119 (mp) cc_final: 0.7916 (mp)
REVERT: B  752 ILE cc_start: 0.8363 (tt) cc_final: 0.7751 (mm)
  outliers start: 19
  outliers final: 19
  residues processed: 146
  average time/residue: 0.2194
  time to fit residues: 46.8072
Evaluate side-chains
  147 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  690 ASP
Chi-restraints excluded: chain B residue  717 VAL
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 111 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 100 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 123 optimal weight:    0.8980
   chunk 139 optimal weight:    2.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 206 GLN
B 692 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.193244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.154535 restraints weight = 14258.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 1.83
r_work: 0.3697 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3568 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  11762  Z= 0.134
  Angle     :  0.585   9.346  15928  Z= 0.299
  Chirality :  0.041   0.202   1754
  Planarity :  0.003   0.032   1998
  Dihedral  :  4.128  16.574   1546
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.34 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.22), residues: 1382
  helix:  1.56 (0.18), residues: 858
  sheet: -3.41 (0.58), residues: 58
  loop : -1.98 (0.25), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 427 
 HIS   0.005   0.001   HIS B 402 
 PHE   0.018   0.001   PHE B 126 
 TYR   0.011   0.001   TYR A 838 
 ARG   0.003   0.000   ARG B 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03811 (  661)
  hydrogen bonds       : angle       3.97751 ( 1947)
  SS BOND              : bond        0.00251 (    8)
  SS BOND              : angle       1.85521 (   16)
  covalent geometry    : bond        0.00314 (11754)
  covalent geometry    : angle       0.58195 (15912)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 1.289 
Fit side-chains
REVERT: A  215 GLN cc_start: 0.7170 (pp30) cc_final: 0.6881 (pt0)
REVERT: A  752 ILE cc_start: 0.8451 (tt) cc_final: 0.7896 (mm)
REVERT: A  909 MET cc_start: 0.4774 (ttm) cc_final: 0.3622 (tpt)
REVERT: B  752 ILE cc_start: 0.8295 (tt) cc_final: 0.7682 (mm)
  outliers start: 20
  outliers final: 19
  residues processed: 145
  average time/residue: 0.2528
  time to fit residues: 54.7221
Evaluate side-chains
  147 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  690 ASP
Chi-restraints excluded: chain B residue  717 VAL
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 138 optimal weight:    5.9990
   chunk 132 optimal weight:    0.8980
   chunk 120 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 102 optimal weight:    0.8980
   chunk 104 optimal weight:    8.9990
   chunk 66 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 115 optimal weight:    0.6980
   chunk 44 optimal weight:   10.0000
   chunk 21 optimal weight:    5.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.193689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.153365 restraints weight = 14137.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3911 rms_B_bonded: 1.70
r_work: 0.3721 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3604 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  11762  Z= 0.133
  Angle     :  0.588   9.506  15928  Z= 0.300
  Chirality :  0.041   0.202   1754
  Planarity :  0.003   0.031   1998
  Dihedral  :  4.072  16.470   1546
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.66 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.22), residues: 1382
  helix:  1.60 (0.17), residues: 858
  sheet: -3.44 (0.57), residues: 58
  loop : -1.96 (0.25), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 427 
 HIS   0.004   0.001   HIS B 402 
 PHE   0.018   0.001   PHE B 126 
 TYR   0.011   0.001   TYR A 687 
 ARG   0.002   0.000   ARG A 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03759 (  661)
  hydrogen bonds       : angle       3.98349 ( 1947)
  SS BOND              : bond        0.00237 (    8)
  SS BOND              : angle       1.79363 (   16)
  covalent geometry    : bond        0.00311 (11754)
  covalent geometry    : angle       0.58604 (15912)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6177.78 seconds
wall clock time: 108 minutes 0.86 seconds (6480.86 seconds total)