Starting phenix.real_space_refine
on Wed Feb 12 19:12:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8irj_35676/02_2025/8irj_35676.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8irj_35676/02_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_35676/02_2025/8irj_35676.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8irj_35676/02_2025/8irj_35676.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8irj_35676/02_2025/8irj_35676.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8irj_35676/02_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-5592/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: 8.16, per 1000 atoms: 0.99
  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=7, 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 445 " - pdb=" SG  CYS A 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: 1.81
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.92
  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: 2.54

  Time building geometry restraints manager: 2.14 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: 4492
       17.96 -    35.91: 394
       35.91 -    53.87: 73
       53.87 -    71.82: 12
       71.82 -    89.78: 10
  Dihedral angle restraints: 4981
    sinusoidal: 1937
      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 4978 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:
        2.03 -     2.60: 66
        2.60 -     3.18: 7029
        3.18 -     3.75: 12067
        3.75 -     4.33: 16169
        4.33 -     4.90: 26699
  Nonbonded interactions: 62030
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B 295 "
            pdb=" SG  CYS B 317 "
     model   vdw
     2.027 3.760
  nonbonded pdb=" SG  CYS B 282 "
            pdb=" SG  CYS B 302 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS B  76 "
            pdb=" SG  CYS B 236 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS B 445 "
            pdb=" SG  CYS B 537 "
     model   vdw
     2.033 3.760
  nonbonded pdb=" SG  CYS B 363 "
            pdb=" SG  CYS B 372 "
     model   vdw
     2.035 3.760
  ... (remaining 62025 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:             4.240
  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:         0.050
  Set scattering table:                    0.070
  Process input model:                     24.010
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.950
-------------------------------------------------------------------------------
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   8426  Z= 0.482
  Angle     :  1.097  12.798  11464  Z= 0.681
  Chirality :  0.063   0.678   1308
  Planarity :  0.007   0.060   1456
  Dihedral  : 14.433  89.775   3000
  Min Nonbonded Distance : 2.027

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 

*********************** 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  : 0.853 
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: 0.2107
  time to fit residues: 48.7968
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  : 1.574 
-------------------------------------------------------------------------------
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:    1.9990
   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:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0670
   chunk 61 optimal weight:    0.7980
   chunk 96 optimal weight:    0.8980
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
A 388 GLN
A 519 HIS
B 388 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.150333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.128598 restraints weight = 15705.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 3.27
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6971
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8426  Z= 0.245
  Angle     :  0.765  12.541  11464  Z= 0.372
  Chirality :  0.042   0.139   1308
  Planarity :  0.006   0.064   1456
  Dihedral  :  5.098  32.984   1156
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 10.00 %
    Favored  : 87.82 %
  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: -0.88 (0.25), residues: 1034
  helix:  0.68 (0.23), residues: 468
  sheet: -0.16 (0.43), residues: 158
  loop : -2.30 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 508 
 HIS   0.003   0.001   HIS A 538 
 PHE   0.020   0.001   PHE B 253 
 TYR   0.021   0.002   TYR B 468 
 ARG   0.004   0.000   ARG A  83 

*********************** 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
  179 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 160
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
REVERT: A  404 ARG cc_start: 0.6461 (tpt90) cc_final: 0.5401 (ttt180)
REVERT: B  392 MET cc_start: 0.7589 (mmm) cc_final: 0.7080 (mtp)
  outliers start: 19
  outliers final: 11
  residues processed: 167
  average time/residue: 0.1953
  time to fit residues: 45.0687
Evaluate side-chains
  147 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
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  373 LEU
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  501 VAL
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:    0.7980
   chunk 14 optimal weight:    0.1980
   chunk 78 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 89 optimal weight:    0.5980
   chunk 85 optimal weight:    4.9990
   chunk 77 optimal weight:    0.0980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4134 r_free = 0.4134 target = 0.149753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 107)---------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.113573 restraints weight = 16096.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 2.01
r_work: 0.3429 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.3084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8426  Z= 0.204
  Angle     :  0.698  13.228  11464  Z= 0.339
  Chirality :  0.041   0.143   1308
  Planarity :  0.005   0.052   1456
  Dihedral  :  4.633  19.301   1150
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.32 %
    Favored  : 81.03 %
  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: -0.46 (0.26), residues: 1034
  helix:  1.16 (0.23), residues: 458
  sheet: -0.15 (0.42), residues: 164
  loop : -2.13 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 450 
 HIS   0.002   0.000   HIS A 519 
 PHE   0.022   0.001   PHE B 434 
 TYR   0.018   0.001   TYR B 468 
 ARG   0.007   0.000   ARG A 240 

*********************** 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
  169 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.850 
Fit side-chains
REVERT: A  404 ARG cc_start: 0.6294 (tpt90) cc_final: 0.4960 (ttt180)
REVERT: B  392 MET cc_start: 0.7856 (mmm) cc_final: 0.7540 (mtp)
REVERT: B  407 ARG cc_start: 0.5538 (mmm160) cc_final: 0.5328 (mtp180)
  outliers start: 23
  outliers final: 13
  residues processed: 153
  average time/residue: 0.2050
  time to fit residues: 43.2702
Evaluate side-chains
  138 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
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  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  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:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.4111 r_free = 0.4111 target = 0.151144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.120892 restraints weight = 16156.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 1.92
r_work: 0.3378 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.3654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8426  Z= 0.265
  Angle     :  0.754  12.803  11464  Z= 0.363
  Chirality :  0.043   0.143   1308
  Planarity :  0.005   0.048   1456
  Dihedral  :  4.764  18.624   1150
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.74 %
    Favored  : 77.82 %
  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: -0.46 (0.26), residues: 1034
  helix:  1.13 (0.24), residues: 468
  sheet: -0.26 (0.41), residues: 166
  loop : -2.12 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 450 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.025   0.002   PHE B 434 
 TYR   0.014   0.002   TYR B 468 
 ARG   0.006   0.000   ARG A 240 

*********************** 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
  169 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.950 
Fit side-chains
REVERT: A  112 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8405 (tp)
REVERT: A  376 GLU cc_start: 0.7374 (tt0) cc_final: 0.7019 (mp0)
REVERT: A  404 ARG cc_start: 0.6460 (tpt90) cc_final: 0.5185 (ttt180)
REVERT: A  452 ARG cc_start: 0.7885 (tpt170) cc_final: 0.7504 (tpp80)
REVERT: B  392 MET cc_start: 0.8159 (mmm) cc_final: 0.7835 (mtp)
  outliers start: 30
  outliers final: 17
  residues processed: 154
  average time/residue: 0.2040
  time to fit residues: 43.5567
Evaluate side-chains
  148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
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  312 LEU
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  599 VAL
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  431 PHE
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  522 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:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 102 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4107 r_free = 0.4107 target = 0.150942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 106)---------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.118759 restraints weight = 16059.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 1.99
r_work: 0.3379 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.4082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8426  Z= 0.235
  Angle     :  0.735  12.605  11464  Z= 0.346
  Chirality :  0.041   0.153   1308
  Planarity :  0.005   0.050   1456
  Dihedral  :  4.596  20.102   1150
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 21.38 %
    Favored  : 75.40 %
  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: -0.40 (0.26), residues: 1034
  helix:  1.27 (0.23), residues: 468
  sheet: -0.38 (0.41), residues: 170
  loop : -2.15 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 450 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.020   0.002   PHE B 504 
 TYR   0.010   0.001   TYR A  80 
 ARG   0.004   0.000   ARG A  83 

*********************** 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
  164 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 0.867 
Fit side-chains
REVERT: A  112 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8332 (tp)
REVERT: A  376 GLU cc_start: 0.7396 (tt0) cc_final: 0.7074 (mp0)
REVERT: A  392 MET cc_start: 0.7789 (mmt) cc_final: 0.7315 (mtp)
REVERT: A  404 ARG cc_start: 0.6385 (tpt90) cc_final: 0.5130 (ttt180)
REVERT: A  426 PHE cc_start: 0.8742 (m-80) cc_final: 0.8444 (m-80)
REVERT: A  452 ARG cc_start: 0.7851 (tpt170) cc_final: 0.7466 (tpp80)
REVERT: A  598 LEU cc_start: 0.9102 (mm) cc_final: 0.8893 (mt)
REVERT: B  392 MET cc_start: 0.8070 (mmm) cc_final: 0.7816 (mtp)
REVERT: B  537 CYS cc_start: 0.7355 (OUTLIER) cc_final: 0.7101 (m)
REVERT: B  625 LEU cc_start: 0.8692 (mp) cc_final: 0.8459 (mt)
  outliers start: 28
  outliers final: 18
  residues processed: 151
  average time/residue: 0.1899
  time to fit residues: 40.2228
Evaluate side-chains
  148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
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  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  501 VAL
Chi-restraints excluded: chain A residue  522 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  270 MET
Chi-restraints excluded: chain B residue  319 CYS
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  537 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 84 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.4090 r_free = 0.4090 target = 0.149527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.119539 restraints weight = 16145.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 1.85
r_work: 0.3364 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.4351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8426  Z= 0.256
  Angle     :  0.740  12.133  11464  Z= 0.353
  Chirality :  0.042   0.158   1308
  Planarity :  0.005   0.037   1456
  Dihedral  :  4.661  19.940   1150
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 20.57 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.26), residues: 1034
  helix:  1.40 (0.23), residues: 476
  sheet: -0.40 (0.40), residues: 170
  loop : -2.15 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 182 
 HIS   0.002   0.001   HIS B 519 
 PHE   0.022   0.002   PHE A 434 
 TYR   0.010   0.001   TYR A  80 
 ARG   0.006   0.000   ARG B  83 

*********************** 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
  177 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 139
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A  112 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8346 (tp)
REVERT: A  376 GLU cc_start: 0.7356 (tt0) cc_final: 0.7095 (mp0)
REVERT: A  392 MET cc_start: 0.7913 (mmt) cc_final: 0.7468 (mtp)
REVERT: A  404 ARG cc_start: 0.6492 (tpt90) cc_final: 0.5221 (ttt180)
REVERT: A  452 ARG cc_start: 0.7875 (tpt170) cc_final: 0.7485 (tpp80)
REVERT: A  577 MET cc_start: 0.7424 (mtt) cc_final: 0.7178 (mtt)
REVERT: B  392 MET cc_start: 0.8180 (mmm) cc_final: 0.7944 (mtp)
REVERT: B  404 ARG cc_start: 0.6399 (tpt170) cc_final: 0.5100 (ttt180)
REVERT: B  452 ARG cc_start: 0.7802 (tpt170) cc_final: 0.7455 (tpp80)
REVERT: B  537 CYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6980 (m)
  outliers start: 38
  outliers final: 24
  residues processed: 158
  average time/residue: 0.1971
  time to fit residues: 43.1382
Evaluate side-chains
  161 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
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  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  467 LEU
Chi-restraints excluded: chain A residue  501 VAL
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  238 GLU
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  319 CYS
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  537 CYS
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:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   chunk 101 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.4067 r_free = 0.4067 target = 0.147703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.124349 restraints weight = 16071.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 3.02
r_work: 0.3285 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.4672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8426  Z= 0.312
  Angle     :  0.782  12.553  11464  Z= 0.374
  Chirality :  0.043   0.153   1308
  Planarity :  0.005   0.039   1456
  Dihedral  :  4.816  20.017   1150
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 20.23 %
    Favored  : 74.83 %
  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: -0.24 (0.26), residues: 1034
  helix:  1.40 (0.23), residues: 480
  sheet: -0.47 (0.41), residues: 170
  loop : -2.08 (0.29), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 450 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.024   0.002   PHE A 253 
 TYR   0.011   0.002   TYR A  80 
 ARG   0.006   0.000   ARG A  83 

*********************** 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
  178 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 135
  time to evaluate  : 0.975 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.8891 (tt) cc_final: 0.8342 (mt)
REVERT: A  112 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8368 (tp)
REVERT: A  392 MET cc_start: 0.8204 (mmt) cc_final: 0.7698 (mtp)
REVERT: A  404 ARG cc_start: 0.6639 (tpt90) cc_final: 0.5400 (ttt180)
REVERT: A  450 TRP cc_start: 0.7778 (m100) cc_final: 0.7288 (m100)
REVERT: A  452 ARG cc_start: 0.7990 (tpt170) cc_final: 0.7604 (tpp80)
REVERT: A  454 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7218 (mm)
REVERT: A  577 MET cc_start: 0.7611 (mtt) cc_final: 0.7360 (mtt)
REVERT: B  392 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7612 (mtt)
REVERT: B  404 ARG cc_start: 0.6545 (tpt170) cc_final: 0.5576 (ttt180)
REVERT: B  452 ARG cc_start: 0.7829 (tpt170) cc_final: 0.7552 (tpp80)
REVERT: B  616 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7375 (t70)
  outliers start: 43
  outliers final: 28
  residues processed: 159
  average time/residue: 0.2014
  time to fit residues: 43.8440
Evaluate side-chains
  163 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue   71 LEU
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  395 ILE
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  454 LEU
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  545 ILE
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  618 THR
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  238 GLU
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain B residue  408 ASN
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  545 ILE
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  616 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 85 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0030
   chunk 30 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.6190

-------------------------------------------------------------------------------
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 = 0.149402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.115140 restraints weight = 16147.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 2.08
r_work: 0.3321 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.4804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8426  Z= 0.212
  Angle     :  0.745  14.304  11464  Z= 0.348
  Chirality :  0.041   0.153   1308
  Planarity :  0.005   0.073   1456
  Dihedral  :  4.563  19.983   1150
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 21.84 %
    Favored  : 74.71 %
  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: -0.13 (0.26), residues: 1034
  helix:  1.48 (0.23), residues: 480
  sheet: -0.14 (0.43), residues: 150
  loop : -2.08 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 450 
 HIS   0.003   0.001   HIS B 533 
 PHE   0.019   0.001   PHE A 253 
 TYR   0.010   0.001   TYR A  80 
 ARG   0.007   0.000   ARG B  83 

*********************** 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
  169 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.8985 (tt) cc_final: 0.8345 (mt)
REVERT: A  112 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8289 (tp)
REVERT: A  392 MET cc_start: 0.8014 (mmt) cc_final: 0.7560 (mtp)
REVERT: A  404 ARG cc_start: 0.6368 (tpt90) cc_final: 0.5136 (ttt180)
REVERT: A  450 TRP cc_start: 0.7953 (m100) cc_final: 0.7620 (m100)
REVERT: A  452 ARG cc_start: 0.7884 (tpt170) cc_final: 0.7468 (tpp80)
REVERT: A  577 MET cc_start: 0.7268 (mtt) cc_final: 0.7059 (mtt)
REVERT: B   60 LEU cc_start: 0.9013 (tt) cc_final: 0.8483 (mt)
REVERT: B  392 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7509 (mtt)
REVERT: B  404 ARG cc_start: 0.6138 (tpt170) cc_final: 0.5213 (ttt180)
REVERT: B  452 ARG cc_start: 0.7810 (tpt170) cc_final: 0.7434 (tpp80)
  outliers start: 30
  outliers final: 23
  residues processed: 155
  average time/residue: 0.1959
  time to fit residues: 42.3698
Evaluate side-chains
  158 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
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  300 THR
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  366 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  501 VAL
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  127 VAL
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  319 CYS
Chi-restraints excluded: chain B residue  392 MET
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 40 optimal weight:    7.9990
   chunk 69 optimal weight:    0.0770
   chunk 90 optimal weight:    0.5980
   chunk 93 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 = 0.4088 r_free = 0.4088 target = 0.150023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.115243 restraints weight = 16272.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.01
r_work: 0.3323 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.4937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8426  Z= 0.204
  Angle     :  0.736  14.666  11464  Z= 0.344
  Chirality :  0.041   0.149   1308
  Planarity :  0.005   0.073   1456
  Dihedral  :  4.460  20.135   1150
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 22.18 %
    Favored  : 74.14 %
  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: -0.06 (0.26), residues: 1034
  helix:  1.51 (0.23), residues: 482
  sheet: -0.33 (0.40), residues: 170
  loop : -1.98 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 450 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.020   0.002   PHE B 504 
 TYR   0.008   0.001   TYR A  80 
 ARG   0.008   0.000   ARG B  83 

*********************** 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
  171 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 139
  time to evaluate  : 0.866 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.8973 (tt) cc_final: 0.8356 (mt)
REVERT: A  112 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8263 (tp)
REVERT: A  392 MET cc_start: 0.7985 (mmt) cc_final: 0.7568 (mtp)
REVERT: A  404 ARG cc_start: 0.6457 (tpt90) cc_final: 0.5212 (ttt180)
REVERT: A  452 ARG cc_start: 0.7855 (tpt170) cc_final: 0.7471 (tpp80)
REVERT: B   60 LEU cc_start: 0.8977 (tt) cc_final: 0.8444 (mt)
REVERT: B  392 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7801 (mtp)
REVERT: B  404 ARG cc_start: 0.6233 (tpt170) cc_final: 0.5304 (ttt180)
REVERT: B  452 ARG cc_start: 0.7799 (tpt170) cc_final: 0.7454 (tpp80)
REVERT: B  454 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7340 (mm)
  outliers start: 32
  outliers final: 24
  residues processed: 155
  average time/residue: 0.2031
  time to fit residues: 43.6196
Evaluate side-chains
  158 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
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  300 THR
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  431 PHE
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 B residue  127 VAL
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  319 CYS
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  454 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  581 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 7 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 103 optimal weight:    0.3980
   chunk 10 optimal weight:    0.0050
   chunk 97 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
B 161 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.150537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.117335 restraints weight = 16015.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 2.05
r_work: 0.3348 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.5026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8426  Z= 0.185
  Angle     :  0.736  15.076  11464  Z= 0.342
  Chirality :  0.041   0.157   1308
  Planarity :  0.005   0.068   1456
  Dihedral  :  4.356  20.249   1150
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 23.91 %
    Favored  : 73.33 %
  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:  0.01 (0.26), residues: 1034
  helix:  1.52 (0.23), residues: 484
  sheet:  0.06 (0.43), residues: 150
  loop : -2.00 (0.28), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 450 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.036   0.001   PHE B 504 
 TYR   0.010   0.001   TYR A  80 
 ARG   0.008   0.000   ARG B  83 

********************** 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
  158 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 0.864 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.8982 (tt) cc_final: 0.8360 (mt)
REVERT: A   70 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7275 (tt0)
REVERT: A  112 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8233 (tp)
REVERT: A  392 MET cc_start: 0.7918 (mmt) cc_final: 0.7521 (mtp)
REVERT: A  404 ARG cc_start: 0.6463 (tpt90) cc_final: 0.5188 (ttt180)
REVERT: A  452 ARG cc_start: 0.7868 (tpt170) cc_final: 0.7514 (tpp80)
REVERT: B   60 LEU cc_start: 0.8950 (tt) cc_final: 0.8421 (mt)
REVERT: B  392 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7816 (mtp)
REVERT: B  404 ARG cc_start: 0.6447 (tpt170) cc_final: 0.5443 (ttt180)
REVERT: B  452 ARG cc_start: 0.7789 (tpt170) cc_final: 0.7456 (tpp80)
REVERT: B  454 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7298 (mm)
  outliers start: 24
  outliers final: 20
  residues processed: 147
  average time/residue: 0.2007
  time to fit residues: 41.0717
Evaluate side-chains
  149 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
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  236 CYS
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  127 VAL
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  319 CYS
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  454 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 96 optimal weight:    0.0170
   chunk 39 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0060
   chunk 54 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0170
   overall best weight:    0.2672

-------------------------------------------------------------------------------
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 = 0.4128 r_free = 0.4128 target = 0.151813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.126708 restraints weight = 16139.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 2.76
r_work: 0.3378 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.5159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8426  Z= 0.164
  Angle     :  0.717  15.117  11464  Z= 0.331
  Chirality :  0.040   0.150   1308
  Planarity :  0.005   0.067   1456
  Dihedral  :  4.161  19.263   1150
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 24.83 %
    Favored  : 72.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.26), residues: 1034
  helix:  1.66 (0.23), residues: 484
  sheet:  0.13 (0.44), residues: 146
  loop : -1.86 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 450 
 HIS   0.002   0.001   HIS A 533 
 PHE   0.034   0.002   PHE B 504 
 TYR   0.013   0.001   TYR A 437 
 ARG   0.008   0.000   ARG B  83 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4520.76 seconds
wall clock time: 80 minutes 45.66 seconds (4845.66 seconds total)