Starting phenix.real_space_refine
on Sun May 11 17:07:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8irj_35676/05_2025/8irj_35676.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8irj_35676/05_2025/8irj_35676.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8irj_35676/05_2025/8irj_35676.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8irj_35676/05_2025/8irj_35676.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8irj_35676/05_2025/8irj_35676.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8irj_35676/05_2025/8irj_35676.cif"
  }
  resolution = 3.49
  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=   0.005 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    5314      2.51       5
     N    1422      2.21       5
     O    1438      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 8228
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 531, 4114
          Classifications: {'peptide': 531}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 30, 'TRANS': 500}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 21
  Restraints were copied for chains:
    B
  Time building chain proxies: 7.49, per 1000 atoms: 0.91
  Number of scatterers: 8228
  At special positions: 0
  Unit cell: (66.3966, 96.1899, 167.694, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1438      8.00
     N    1422      7.00
     C    5314      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  76 " - pdb=" SG  CYS A 236 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 282 " - pdb=" SG  CYS A 302 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 295 " - pdb=" SG  CYS A 317 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 319 " - pdb=" SG  CYS A 356 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 359 " - pdb=" SG  CYS A 366 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 363 " - pdb=" SG  CYS A 372 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 390 " - pdb=" SG  CYS B 390 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 445 " - pdb=" SG  CYS A 537 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  76 " - pdb=" SG  CYS B 236 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 282 " - pdb=" SG  CYS B 302 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 295 " - pdb=" SG  CYS B 317 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 319 " - pdb=" SG  CYS B 356 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 359 " - pdb=" SG  CYS B 366 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 363 " - pdb=" SG  CYS B 372 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 445 " - pdb=" SG  CYS B 537 " 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: 1.86
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1960

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 10 sheets defined
      50.5% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 63
    Processing helix  chain 'A' and resid 68 through 72
    Processing helix  chain 'A' and resid 92 through 116
      removed outlier: 3.603A  pdb=" N   THR A 101 " --> pdb=" O   GLY A  97 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLN A 104 " --> pdb=" O   GLY A 100 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ALA A 105 " --> pdb=" O   THR A 101 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ALA A 106 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 139
      removed outlier: 3.842A  pdb=" N   TYR A 130 " --> pdb=" O   ASP A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 227
    Processing helix  chain 'A' and resid 328 through 332
    Processing helix  chain 'A' and resid 378 through 402
      removed outlier: 3.861A  pdb=" N   ALA A 382 " --> pdb=" O   ALA A 378 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   CYS A 391 " --> pdb=" O   CYS A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 408
      removed outlier: 3.980A  pdb=" N   ARG A 407 " --> pdb=" O   TYR A 403 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ASN A 408 " --> pdb=" O   ARG A 404 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 403 through 408'
    Processing helix  chain 'A' and resid 416 through 431
      removed outlier: 3.559A  pdb=" N   PHE A 431 " --> pdb=" O   LEU A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 436
    Processing helix  chain 'A' and resid 441 through 475
      removed outlier: 3.870A  pdb=" N   THR A 462 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   LEU A 475 " --> pdb=" O   LEU A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 519
      Proline residue:  A 500  - end of helix
    Processing helix  chain 'A' and resid 540 through 565
      removed outlier: 3.570A  pdb=" N   GLY A 557 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   THR A 564 " --> pdb=" O   LEU A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 599
      removed outlier: 3.980A  pdb=" N   TYR A 576 " --> pdb=" O   HIS A 572 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   MET A 577 " --> pdb=" O   GLU A 573 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ILE A 579 " --> pdb=" O   ARG A 575 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA A 580 " --> pdb=" O   TYR A 576 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   VAL A 597 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'A' and resid 603 through 632
      Proline residue:  A 629  - end of helix
      removed outlier: 3.657A  pdb=" N   TRP A 632 " --> pdb=" O   ILE A 628 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 63
    Processing helix  chain 'B' and resid 68 through 72
    Processing helix  chain 'B' and resid 92 through 116
      removed outlier: 3.602A  pdb=" N   THR B 101 " --> pdb=" O   GLY B  97 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLN B 104 " --> pdb=" O   GLY B 100 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ALA B 105 " --> pdb=" O   THR B 101 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ALA B 106 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 139
      removed outlier: 3.842A  pdb=" N   TYR B 130 " --> pdb=" O   ASP B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 227
    Processing helix  chain 'B' and resid 328 through 332
    Processing helix  chain 'B' and resid 378 through 402
      removed outlier: 3.862A  pdb=" N   ALA B 382 " --> pdb=" O   ALA B 378 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   CYS B 391 " --> pdb=" O   CYS B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 408
      removed outlier: 3.980A  pdb=" N   ARG B 407 " --> pdb=" O   TYR B 403 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASN B 408 " --> pdb=" O   ARG B 404 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 403 through 408'
    Processing helix  chain 'B' and resid 416 through 431
      removed outlier: 3.559A  pdb=" N   PHE B 431 " --> pdb=" O   LEU B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 436
    Processing helix  chain 'B' and resid 441 through 475
      removed outlier: 3.869A  pdb=" N   THR B 462 " --> pdb=" O   ILE B 458 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   LEU B 475 " --> pdb=" O   LEU B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 519
      Proline residue:  B 500  - end of helix
    Processing helix  chain 'B' and resid 540 through 565
      removed outlier: 3.571A  pdb=" N   GLY B 557 " --> pdb=" O   LEU B 553 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   THR B 564 " --> pdb=" O   LEU B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 599
      removed outlier: 3.979A  pdb=" N   TYR B 576 " --> pdb=" O   HIS B 572 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   MET B 577 " --> pdb=" O   GLU B 573 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ILE B 579 " --> pdb=" O   ARG B 575 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA B 580 " --> pdb=" O   TYR B 576 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   VAL B 597 " --> pdb=" O   THR B 593 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 602
      No H-bonds generated for 'chain 'B' and resid 600 through 602'
    Processing helix  chain 'B' and resid 603 through 632
      Proline residue:  B 629  - end of helix
      removed outlier: 3.658A  pdb=" N   TRP B 632 " --> pdb=" O   ILE B 628 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81
      removed outlier: 3.910A  pdb=" N   TYR A  80 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 229
      removed outlier: 3.852A  pdb=" N   PHE A 253 " --> pdb=" O   GLY A 266 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLY A 266 " --> pdb=" O   PHE A 253 " (cutoff:3.500A)
      removed outlier: 8.371A  pdb=" N   ARG A 265 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   PHE A 151 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   GLN A 267 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   LEU A 149 " --> pdb=" O   GLN A 267 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   GLN A 269 " --> pdb=" O   ALA A 147 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   ALA A 147 " --> pdb=" O   GLN A 269 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   ASP A 271 " --> pdb=" O   TYR A 145 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   LEU A 162 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR B 203 " --> pdb=" O   THR A 173 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 221
      removed outlier: 7.872A  pdb=" N   THR B 173 " --> pdb=" O   LYS A 199 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   VAL A 201 " --> pdb=" O   THR B 173 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   LEU B 175 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   THR A 203 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   LEU B 162 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ASP B 271 " --> pdb=" O   TYR B 145 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   ALA B 147 " --> pdb=" O   GLN B 269 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   GLN B 269 " --> pdb=" O   ALA B 147 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   LEU B 149 " --> pdb=" O   GLN B 267 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   GLN B 267 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   PHE B 151 " --> pdb=" O   ARG B 265 " (cutoff:3.500A)
      removed outlier: 8.371A  pdb=" N   ARG B 265 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLY B 266 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   PHE B 253 " --> pdb=" O   GLY B 266 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 236 through 237
    Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 304
    Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 527
      removed outlier: 3.764A  pdb=" N   PHE A 534 " --> pdb=" O   GLY A 526 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 80 through 81
      removed outlier: 3.909A  pdb=" N   TYR B  80 " --> pdb=" O   LEU B 234 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 236 through 237
    Processing sheet with id=AA9, first strand: chain 'B' and resid 300 through 304
    Processing sheet with id=AB1, first strand: chain 'B' and resid 526 through 527
      removed outlier: 3.763A  pdb=" N   PHE B 534 " --> pdb=" O   GLY B 526 " (cutoff:3.500A)

    430 hydrogen bonds defined for protein.
    1230 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: 2.17

  Time building geometry restraints manager: 2.23 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2482
        1.34 -     1.46: 1974
        1.46 -     1.58: 3900
        1.58 -     1.71: 2
        1.71 -     1.83: 68
  Bond restraints: 8426
  Sorted by residual:
  bond pdb=" C   GLN A 225 "
       pdb=" N   GLN A 226 "
    ideal  model  delta    sigma   weight residual
    1.335  1.411 -0.076 1.33e-02 5.65e+03 3.31e+01
  bond pdb=" C   GLN B 225 "
       pdb=" N   GLN B 226 "
    ideal  model  delta    sigma   weight residual
    1.335  1.411 -0.076 1.33e-02 5.65e+03 3.29e+01
  bond pdb=" C   LEU A 473 "
       pdb=" N   PHE A 474 "
    ideal  model  delta    sigma   weight residual
    1.334  1.389 -0.055 1.27e-02 6.20e+03 1.89e+01
  bond pdb=" C   LEU B 473 "
       pdb=" N   PHE B 474 "
    ideal  model  delta    sigma   weight residual
    1.334  1.389 -0.055 1.27e-02 6.20e+03 1.86e+01
  bond pdb=" N   VAL B 523 "
       pdb=" CA  VAL B 523 "
    ideal  model  delta    sigma   weight residual
    1.456  1.499 -0.043 1.23e-02 6.61e+03 1.25e+01
  ... (remaining 8421 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 10955
        2.56 -     5.12: 455
        5.12 -     7.68: 48
        7.68 -    10.24: 4
       10.24 -    12.80: 2
  Bond angle restraints: 11464
  Sorted by residual:
  angle pdb=" N   PRO A 521 "
        pdb=" CA  PRO A 521 "
        pdb=" C   PRO A 521 "
      ideal   model   delta    sigma   weight residual
     113.65  100.85   12.80 1.35e+00 5.49e-01 8.99e+01
  angle pdb=" N   PRO B 521 "
        pdb=" CA  PRO B 521 "
        pdb=" C   PRO B 521 "
      ideal   model   delta    sigma   weight residual
     113.65  100.87   12.78 1.35e+00 5.49e-01 8.96e+01
  angle pdb=" N   ARG B 406 "
        pdb=" CA  ARG B 406 "
        pdb=" C   ARG B 406 "
      ideal   model   delta    sigma   weight residual
     114.62  106.47    8.15 1.14e+00 7.69e-01 5.12e+01
  angle pdb=" N   ARG A 406 "
        pdb=" CA  ARG A 406 "
        pdb=" C   ARG A 406 "
      ideal   model   delta    sigma   weight residual
     114.62  106.50    8.12 1.14e+00 7.69e-01 5.07e+01
  angle pdb=" C   ARG A 525 "
        pdb=" CA  ARG A 525 "
        pdb=" CB  ARG A 525 "
      ideal   model   delta    sigma   weight residual
     110.34  118.05   -7.71 1.40e+00 5.10e-01 3.03e+01
  ... (remaining 11459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4504
       17.96 -    35.91: 403
       35.91 -    53.87: 76
       53.87 -    71.82: 12
       71.82 -    89.78: 10
  Dihedral angle restraints: 5005
    sinusoidal: 1961
      harmonic: 3044
  Sorted by residual:
  dihedral pdb=" CA  PHE B 431 "
           pdb=" C   PHE B 431 "
           pdb=" N   PRO B 432 "
           pdb=" CA  PRO B 432 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.66  -29.34     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" CA  PHE A 431 "
           pdb=" C   PHE A 431 "
           pdb=" N   PRO A 432 "
           pdb=" CA  PRO A 432 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.68  -29.32     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" CA  SER A 486 "
           pdb=" C   SER A 486 "
           pdb=" N   SER A 487 "
           pdb=" CA  SER A 487 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.52   25.48     0      5.00e+00 4.00e-02 2.60e+01
  ... (remaining 5002 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.136: 1273
       0.136 -    0.271: 27
       0.271 -    0.407: 6
       0.407 -    0.542: 0
       0.542 -    0.678: 2
  Chirality restraints: 1308
  Sorted by residual:
  chirality pdb=" CG  LEU B 428 "
            pdb=" CB  LEU B 428 "
            pdb=" CD1 LEU B 428 "
            pdb=" CD2 LEU B 428 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.91   -0.68 2.00e-01 2.50e+01 1.15e+01
  chirality pdb=" CG  LEU A 428 "
            pdb=" CB  LEU A 428 "
            pdb=" CD1 LEU A 428 "
            pdb=" CD2 LEU A 428 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.92   -0.67 2.00e-01 2.50e+01 1.14e+01
  chirality pdb=" CA  THR B 150 "
            pdb=" N   THR B 150 "
            pdb=" C   THR B 150 "
            pdb=" CB  THR B 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.15    0.38 2.00e-01 2.50e+01 3.52e+00
  ... (remaining 1305 not shown)

  Planarity restraints: 1456
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 585 "   -0.018 2.00e-02 2.50e+03   3.68e-02 1.35e+01
        pdb=" C   LEU A 585 "    0.064 2.00e-02 2.50e+03
        pdb=" O   LEU A 585 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LEU A 586 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 585 "    0.018 2.00e-02 2.50e+03   3.67e-02 1.35e+01
        pdb=" C   LEU B 585 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   LEU B 585 "    0.024 2.00e-02 2.50e+03
        pdb=" N   LEU B 586 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 405 "   -0.013 2.00e-02 2.50e+03   2.59e-02 6.73e+00
        pdb=" C   CYS A 405 "    0.045 2.00e-02 2.50e+03
        pdb=" O   CYS A 405 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ARG A 406 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1453 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1930
        2.80 -     3.32: 7895
        3.32 -     3.85: 12666
        3.85 -     4.37: 14593
        4.37 -     4.90: 24922
  Nonbonded interactions: 62006
  Sorted by model distance:
  nonbonded pdb=" CG  ARG A 541 "
            pdb=" CE3 TRP A 542 "
     model   vdw
     2.274 3.740
  nonbonded pdb=" CG  ARG B 541 "
            pdb=" CE3 TRP B 542 "
     model   vdw
     2.274 3.740
  nonbonded pdb=" CG  ARG A 541 "
            pdb=" CZ3 TRP A 542 "
     model   vdw
     2.314 3.740
  nonbonded pdb=" CG  ARG B 541 "
            pdb=" CZ3 TRP B 542 "
     model   vdw
     2.314 3.740
  nonbonded pdb=" O   LEU A 133 "
            pdb=" OG  SER A 136 "
     model   vdw
     2.368 3.040
  ... (remaining 62001 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: 0.04
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:             2.860
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.980
  Find NCS groups from input model:        0.130
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.076   8441  Z= 0.423
  Angle     :  1.099  12.798  11494  Z= 0.681
  Chirality :  0.063   0.678   1308
  Planarity :  0.007   0.060   1456
  Dihedral  : 14.433  89.775   3000
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  1.84 %
    Favored  : 97.01 %
  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: -1.75 (0.24), residues: 1034
  helix: -0.16 (0.23), residues: 452
  sheet: -0.02 (0.49), residues: 122
  loop : -2.58 (0.25), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 450 
 HIS   0.006   0.001   HIS A 603 
 PHE   0.019   0.002   PHE B 253 
 TYR   0.028   0.002   TYR B 468 
 ARG   0.008   0.001   ARG B 525 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18323 (  430)
  hydrogen bonds       : angle       7.38709 ( 1230)
  SS BOND              : bond        0.00523 (   15)
  SS BOND              : angle       1.57901 (   30)
  covalent geometry    : bond        0.00732 ( 8426)
  covalent geometry    : angle       1.09728 (11464)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 162
  time to evaluate  : 0.935 
Fit side-chains
REVERT: A  452 ARG cc_start: 0.7990 (tpt170) cc_final: 0.7740 (tpp80)
REVERT: B  452 ARG cc_start: 0.7951 (tpt170) cc_final: 0.7724 (tpp80)
  outliers start: 10
  outliers final: 4
  residues processed: 172
  average time/residue: 0.2040
  time to fit residues: 47.1467
Evaluate side-chains
  125 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 121
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  522 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 80 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0670
   chunk 61 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0470
   overall best weight:    0.5216

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

Flipped N/Q/H residues before XYZ refinement:
A 388 GLN
B 388 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.150768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.128228 restraints weight = 15749.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3838 rms_B_bonded: 2.98
r_work: 0.3407 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8441  Z= 0.151
  Angle     :  0.742  12.539  11494  Z= 0.360
  Chirality :  0.041   0.138   1308
  Planarity :  0.006   0.059   1456
  Dihedral  :  5.006  33.665   1156
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  9.77 %
    Favored  : 88.28 %
  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: -0.84 (0.25), residues: 1034
  helix:  0.72 (0.23), residues: 464
  sheet: -0.17 (0.43), residues: 158
  loop : -2.26 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 508 
 HIS   0.002   0.001   HIS A 538 
 PHE   0.019   0.001   PHE B 434 
 TYR   0.022   0.002   TYR B 468 
 ARG   0.004   0.000   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04883 (  430)
  hydrogen bonds       : angle       5.00610 ( 1230)
  SS BOND              : bond        0.00379 (   15)
  SS BOND              : angle       1.22933 (   30)
  covalent geometry    : bond        0.00325 ( 8426)
  covalent geometry    : angle       0.73999 (11464)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 154
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: A  404 ARG cc_start: 0.6398 (tpt90) cc_final: 0.5133 (ttt180)
REVERT: B  376 GLU cc_start: 0.6993 (tt0) cc_final: 0.6753 (mp0)
REVERT: B  392 MET cc_start: 0.8076 (mmm) cc_final: 0.7538 (mtp)
  outliers start: 17
  outliers final: 9
  residues processed: 161
  average time/residue: 0.1936
  time to fit residues: 43.1434
Evaluate side-chains
  143 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 134
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9980
   chunk 87 optimal weight:    0.7980
   chunk 89 optimal weight:    0.6980
   chunk 85 optimal weight:    4.9990
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
B 204 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.147760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 130)---------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.112490 restraints weight = 15910.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 2.02
r_work: 0.3377 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8441  Z= 0.174
  Angle     :  0.740  13.611  11494  Z= 0.362
  Chirality :  0.042   0.176   1308
  Planarity :  0.005   0.050   1456
  Dihedral  :  4.807  19.323   1150
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 16.55 %
    Favored  : 80.34 %
  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: -0.56 (0.26), residues: 1034
  helix:  1.00 (0.23), residues: 468
  sheet: -0.28 (0.43), residues: 160
  loop : -2.10 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 450 
 HIS   0.002   0.001   HIS A 538 
 PHE   0.023   0.002   PHE B 434 
 TYR   0.019   0.002   TYR B 468 
 ARG   0.007   0.000   ARG A 240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05120 (  430)
  hydrogen bonds       : angle       4.88601 ( 1230)
  SS BOND              : bond        0.00436 (   15)
  SS BOND              : angle       1.43813 (   30)
  covalent geometry    : bond        0.00398 ( 8426)
  covalent geometry    : angle       0.73761 (11464)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 152
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A  354 LEU cc_start: 0.5283 (tp) cc_final: 0.4814 (tp)
REVERT: A  376 GLU cc_start: 0.7300 (tt0) cc_final: 0.6911 (mp0)
REVERT: A  404 ARG cc_start: 0.6265 (tpt90) cc_final: 0.4988 (ttt180)
REVERT: A  585 LEU cc_start: 0.8929 (tt) cc_final: 0.8671 (tt)
REVERT: B  376 GLU cc_start: 0.7260 (tt0) cc_final: 0.6921 (mp0)
REVERT: B  392 MET cc_start: 0.7921 (mmm) cc_final: 0.7505 (mtp)
  outliers start: 27
  outliers final: 16
  residues processed: 157
  average time/residue: 0.2043
  time to fit residues: 43.6170
Evaluate side-chains
  143 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue   69 GLN
Chi-restraints excluded: chain B residue   88 MET
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  524 ILE
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  599 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    0.4980
   chunk 34 optimal weight:    0.0870
   chunk 10 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   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 181 ASN
B 204 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.152720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 97)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.118968 restraints weight = 16156.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 1.83
r_work: 0.3406 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.3558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8441  Z= 0.148
  Angle     :  0.717  12.604  11494  Z= 0.344
  Chirality :  0.042   0.155   1308
  Planarity :  0.005   0.042   1456
  Dihedral  :  4.594  18.970   1150
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 18.97 %
    Favored  : 77.36 %
  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: -0.49 (0.26), residues: 1034
  helix:  1.09 (0.23), residues: 468
  sheet: -0.25 (0.42), residues: 166
  loop : -2.13 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 450 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.023   0.001   PHE B 434 
 TYR   0.014   0.001   TYR A 468 
 ARG   0.006   0.000   ARG A 240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04659 (  430)
  hydrogen bonds       : angle       4.75993 ( 1230)
  SS BOND              : bond        0.00415 (   15)
  SS BOND              : angle       1.31442 (   30)
  covalent geometry    : bond        0.00328 ( 8426)
  covalent geometry    : angle       0.71487 (11464)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8341 (tp)
REVERT: A  376 GLU cc_start: 0.7367 (tt0) cc_final: 0.6983 (mp0)
REVERT: A  404 ARG cc_start: 0.6236 (tpt90) cc_final: 0.4984 (ttt180)
REVERT: A  450 TRP cc_start: 0.7959 (m100) cc_final: 0.7601 (m100)
REVERT: B  392 MET cc_start: 0.8100 (mmm) cc_final: 0.7663 (mtp)
  outliers start: 32
  outliers final: 21
  residues processed: 146
  average time/residue: 0.1884
  time to fit residues: 37.9356
Evaluate side-chains
  145 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  204 ASN
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 18 optimal weight:    0.2980
   chunk 57 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 101 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 102 optimal weight:    0.7980
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
B 204 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.151733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.127142 restraints weight = 16013.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 3.04
r_work: 0.3352 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.3800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8441  Z= 0.153
  Angle     :  0.728  12.369  11494  Z= 0.346
  Chirality :  0.042   0.176   1308
  Planarity :  0.004   0.039   1456
  Dihedral  :  4.546  18.920   1150
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 20.46 %
    Favored  : 75.75 %
  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: -0.48 (0.26), residues: 1034
  helix:  1.16 (0.23), residues: 468
  sheet: -0.36 (0.41), residues: 170
  loop : -2.15 (0.28), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 450 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.019   0.001   PHE B 434 
 TYR   0.012   0.001   TYR A 468 
 ARG   0.006   0.000   ARG A 240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04648 (  430)
  hydrogen bonds       : angle       4.71814 ( 1230)
  SS BOND              : bond        0.00449 (   15)
  SS BOND              : angle       1.32195 (   30)
  covalent geometry    : bond        0.00343 ( 8426)
  covalent geometry    : angle       0.72561 (11464)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 139
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8329 (tp)
REVERT: A  376 GLU cc_start: 0.7233 (tt0) cc_final: 0.7024 (mp0)
REVERT: A  404 ARG cc_start: 0.6557 (tpt90) cc_final: 0.5337 (ttt180)
REVERT: A  452 ARG cc_start: 0.7790 (tpt170) cc_final: 0.7422 (tpp80)
REVERT: A  598 LEU cc_start: 0.9049 (mm) cc_final: 0.8837 (mt)
REVERT: B  392 MET cc_start: 0.8158 (mmm) cc_final: 0.7731 (mtp)
REVERT: B  452 ARG cc_start: 0.7769 (tpt170) cc_final: 0.7439 (tpp80)
  outliers start: 33
  outliers final: 21
  residues processed: 154
  average time/residue: 0.2009
  time to fit residues: 41.9552
Evaluate side-chains
  146 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain B residue   88 MET
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  599 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   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 533 HIS
B 204 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.149742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.119064 restraints weight = 16075.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 1.94
r_work: 0.3358 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.4176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8441  Z= 0.176
  Angle     :  0.772  12.127  11494  Z= 0.365
  Chirality :  0.043   0.164   1308
  Planarity :  0.005   0.035   1456
  Dihedral  :  4.683  19.527   1150
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 20.92 %
    Favored  : 74.60 %
  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: -0.41 (0.26), residues: 1034
  helix:  1.26 (0.23), residues: 468
  sheet: -0.40 (0.41), residues: 170
  loop : -2.15 (0.28), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 450 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.022   0.002   PHE A 253 
 TYR   0.010   0.001   TYR A  80 
 ARG   0.007   0.000   ARG A 240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05045 (  430)
  hydrogen bonds       : angle       4.75201 ( 1230)
  SS BOND              : bond        0.00544 (   15)
  SS BOND              : angle       1.52331 (   30)
  covalent geometry    : bond        0.00404 ( 8426)
  covalent geometry    : angle       0.76925 (11464)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 134
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8359 (tp)
REVERT: A  376 GLU cc_start: 0.7395 (tt0) cc_final: 0.7086 (mp0)
REVERT: A  392 MET cc_start: 0.8014 (mmt) cc_final: 0.7635 (mmt)
REVERT: A  404 ARG cc_start: 0.6494 (tpt90) cc_final: 0.5215 (ttt180)
REVERT: A  452 ARG cc_start: 0.7820 (tpt170) cc_final: 0.7439 (tpp80)
REVERT: A  556 TRP cc_start: 0.6614 (t60) cc_final: 0.6400 (t60)
REVERT: B  392 MET cc_start: 0.8271 (mmm) cc_final: 0.7920 (mtp)
REVERT: B  404 ARG cc_start: 0.6435 (tpt170) cc_final: 0.5242 (ttt180)
  outliers start: 39
  outliers final: 28
  residues processed: 154
  average time/residue: 0.2014
  time to fit residues: 42.5054
Evaluate side-chains
  154 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  545 ILE
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain A residue  628 ILE
Chi-restraints excluded: chain B residue   88 MET
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  599 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 105 optimal weight:    0.0870
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.7758

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

Flipped N/Q/H residues before XYZ refinement:
B 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.150069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.126434 restraints weight = 16118.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 3.24
r_work: 0.3307 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.4367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8441  Z= 0.163
  Angle     :  0.749  14.211  11494  Z= 0.356
  Chirality :  0.041   0.145   1308
  Planarity :  0.005   0.034   1456
  Dihedral  :  4.648  29.803   1150
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 22.41 %
    Favored  : 73.45 %
  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: -0.25 (0.26), residues: 1034
  helix:  1.41 (0.23), residues: 476
  sheet: -0.43 (0.41), residues: 170
  loop : -2.10 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 450 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.023   0.002   PHE A 434 
 TYR   0.010   0.001   TYR A  80 
 ARG   0.006   0.000   ARG B  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04750 (  430)
  hydrogen bonds       : angle       4.67448 ( 1230)
  SS BOND              : bond        0.00502 (   15)
  SS BOND              : angle       1.54395 (   30)
  covalent geometry    : bond        0.00374 ( 8426)
  covalent geometry    : angle       0.74581 (11464)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 143
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8323 (tp)
REVERT: A  392 MET cc_start: 0.8032 (mmt) cc_final: 0.7669 (mmt)
REVERT: A  404 ARG cc_start: 0.6585 (tpt90) cc_final: 0.5396 (ttt180)
REVERT: A  452 ARG cc_start: 0.7780 (tpt170) cc_final: 0.7416 (tpp80)
REVERT: B  392 MET cc_start: 0.8217 (mmm) cc_final: 0.7887 (mtp)
REVERT: B  404 ARG cc_start: 0.6534 (tpt170) cc_final: 0.5339 (ttt180)
REVERT: B  450 TRP cc_start: 0.7765 (m100) cc_final: 0.7524 (m100)
REVERT: B  452 ARG cc_start: 0.7782 (tpt170) cc_final: 0.7418 (tpp80)
  outliers start: 36
  outliers final: 23
  residues processed: 159
  average time/residue: 0.1986
  time to fit residues: 43.1620
Evaluate side-chains
  158 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  545 ILE
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain A residue  628 ILE
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  536 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 61 optimal weight:    0.0970
   chunk 8 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 60 optimal weight:    0.4980
   chunk 1 optimal weight:    0.4980
   chunk 30 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.4778

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.151001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.120930 restraints weight = 16187.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 1.93
r_work: 0.3392 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.4514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8441  Z= 0.135
  Angle     :  0.727  14.227  11494  Z= 0.342
  Chirality :  0.041   0.171   1308
  Planarity :  0.004   0.037   1456
  Dihedral  :  4.469  30.701   1150
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 23.10 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.27 (0.26), residues: 1034
  helix:  1.39 (0.23), residues: 480
  sheet: -0.37 (0.40), residues: 182
  loop : -2.22 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 450 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.021   0.001   PHE A 434 
 TYR   0.009   0.001   TYR B  80 
 ARG   0.007   0.000   ARG B  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04290 (  430)
  hydrogen bonds       : angle       4.58523 ( 1230)
  SS BOND              : bond        0.00458 (   15)
  SS BOND              : angle       1.52542 (   30)
  covalent geometry    : bond        0.00293 ( 8426)
  covalent geometry    : angle       0.72370 (11464)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 134
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8278 (tp)
REVERT: A  392 MET cc_start: 0.8057 (mmt) cc_final: 0.7663 (mmt)
REVERT: A  404 ARG cc_start: 0.6457 (tpt90) cc_final: 0.5206 (ttt180)
REVERT: A  452 ARG cc_start: 0.7664 (tpt170) cc_final: 0.7377 (tpp80)
REVERT: B  392 MET cc_start: 0.8116 (mmm) cc_final: 0.7836 (mtp)
REVERT: B  404 ARG cc_start: 0.6397 (tpt170) cc_final: 0.5249 (ttt180)
REVERT: B  452 ARG cc_start: 0.7745 (tpt170) cc_final: 0.7420 (tpp80)
  outliers start: 30
  outliers final: 22
  residues processed: 150
  average time/residue: 0.1967
  time to fit residues: 40.1584
Evaluate side-chains
  147 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  628 ILE
Chi-restraints excluded: chain B residue   88 MET
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  536 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0970
   chunk 90 optimal weight:    0.9980
   chunk 93 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.7778

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

Flipped N/Q/H residues before XYZ refinement:
B 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.149255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.124914 restraints weight = 16262.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 3.55
r_work: 0.3284 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.4644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8441  Z= 0.165
  Angle     :  0.765  14.613  11494  Z= 0.362
  Chirality :  0.042   0.174   1308
  Planarity :  0.005   0.045   1456
  Dihedral  :  4.568  28.421   1150
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 23.22 %
    Favored  : 72.99 %
  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: -0.22 (0.26), residues: 1034
  helix:  1.38 (0.23), residues: 480
  sheet: -0.41 (0.41), residues: 170
  loop : -2.04 (0.28), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 450 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.021   0.002   PHE A 434 
 TYR   0.012   0.001   TYR A  80 
 ARG   0.007   0.000   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04694 (  430)
  hydrogen bonds       : angle       4.65122 ( 1230)
  SS BOND              : bond        0.00442 (   15)
  SS BOND              : angle       1.68016 (   30)
  covalent geometry    : bond        0.00379 ( 8426)
  covalent geometry    : angle       0.76126 (11464)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 134
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.7669 (tm-30) cc_final: 0.7370 (tt0)
REVERT: A  112 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8318 (tp)
REVERT: A  392 MET cc_start: 0.8168 (mmt) cc_final: 0.7836 (mmt)
REVERT: A  404 ARG cc_start: 0.6586 (tpt90) cc_final: 0.5327 (ttt180)
REVERT: A  452 ARG cc_start: 0.7801 (tpt170) cc_final: 0.7495 (tpp80)
REVERT: A  577 MET cc_start: 0.7703 (mtt) cc_final: 0.7490 (mtt)
REVERT: B   60 LEU cc_start: 0.8954 (tt) cc_final: 0.8412 (mt)
REVERT: B  392 MET cc_start: 0.8220 (mmm) cc_final: 0.7773 (mtp)
REVERT: B  404 ARG cc_start: 0.6558 (tpt170) cc_final: 0.5359 (ttt180)
REVERT: B  452 ARG cc_start: 0.7789 (tpt170) cc_final: 0.7477 (tpp80)
  outliers start: 33
  outliers final: 27
  residues processed: 151
  average time/residue: 0.1951
  time to fit residues: 40.4970
Evaluate side-chains
  153 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 125
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  628 ILE
Chi-restraints excluded: chain B residue   88 MET
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.148724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.124188 restraints weight = 16020.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 3.07
r_work: 0.3298 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.4748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8441  Z= 0.173
  Angle     :  0.791  15.552  11494  Z= 0.373
  Chirality :  0.043   0.182   1308
  Planarity :  0.005   0.045   1456
  Dihedral  :  4.632  30.120   1150
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 23.79 %
    Favored  : 72.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.28 (0.26), residues: 1034
  helix:  1.38 (0.23), residues: 480
  sheet: -0.44 (0.40), residues: 184
  loop : -2.20 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 450 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.025   0.002   PHE B 504 
 TYR   0.010   0.001   TYR A  62 
 ARG   0.007   0.000   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04794 (  430)
  hydrogen bonds       : angle       4.67194 ( 1230)
  SS BOND              : bond        0.00474 (   15)
  SS BOND              : angle       1.67646 (   30)
  covalent geometry    : bond        0.00404 ( 8426)
  covalent geometry    : angle       0.78741 (11464)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7271 (tt0)
REVERT: A  112 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8312 (tp)
REVERT: A  404 ARG cc_start: 0.6579 (tpt90) cc_final: 0.5315 (ttt180)
REVERT: A  452 ARG cc_start: 0.7765 (tpt170) cc_final: 0.7453 (tpp80)
REVERT: A  577 MET cc_start: 0.7653 (mtt) cc_final: 0.7419 (mtt)
REVERT: A  616 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7312 (t70)
REVERT: B   60 LEU cc_start: 0.8939 (tt) cc_final: 0.8388 (mt)
REVERT: B  392 MET cc_start: 0.8173 (mmm) cc_final: 0.7705 (mtp)
REVERT: B  404 ARG cc_start: 0.6485 (tpt170) cc_final: 0.5321 (ttt180)
REVERT: B  452 ARG cc_start: 0.7799 (tpt170) cc_final: 0.7454 (tpp80)
  outliers start: 31
  outliers final: 25
  residues processed: 144
  average time/residue: 0.2057
  time to fit residues: 40.3697
Evaluate side-chains
  154 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 127
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  616 HIS
Chi-restraints excluded: chain A residue  628 ILE
Chi-restraints excluded: chain B residue   88 MET
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 81 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0870
   overall best weight:    0.9764

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

Flipped N/Q/H residues before XYZ refinement:
B 533 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.147846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.123335 restraints weight = 16060.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 3.04
r_work: 0.3298 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.4879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8441  Z= 0.188
  Angle     :  0.802  15.413  11494  Z= 0.378
  Chirality :  0.043   0.177   1308
  Planarity :  0.005   0.044   1456
  Dihedral  :  4.664  21.241   1150
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 23.56 %
    Favored  : 72.76 %
  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: -0.30 (0.26), residues: 1034
  helix:  1.37 (0.23), residues: 480
  sheet: -0.60 (0.40), residues: 188
  loop : -2.15 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 508 
 HIS   0.004   0.001   HIS A 533 
 PHE   0.025   0.002   PHE B 504 
 TYR   0.012   0.002   TYR A  80 
 ARG   0.008   0.000   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05055 (  430)
  hydrogen bonds       : angle       4.71058 ( 1230)
  SS BOND              : bond        0.00482 (   15)
  SS BOND              : angle       1.48308 (   30)
  covalent geometry    : bond        0.00441 ( 8426)
  covalent geometry    : angle       0.79941 (11464)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4269.58 seconds
wall clock time: 74 minutes 24.03 seconds (4464.03 seconds total)