Starting phenix.real_space_refine
on Thu Feb 13 19:05:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d67_46588/02_2025/9d67_46588.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d67_46588/02_2025/9d67_46588.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d67_46588/02_2025/9d67_46588.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d67_46588/02_2025/9d67_46588.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d67_46588/02_2025/9d67_46588.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d67_46588/02_2025/9d67_46588.cif"
  }
  resolution = 2.87
  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=   0.003 sd=   0.151
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Hg      3     10.96       5
     S      60      5.16       5
     Na      9      4.78       5
     C    6087      2.51       5
     N    1479      2.21       5
     O    1659      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 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: 9297
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 406, 3085
          Classifications: {'peptide': 406}
          Link IDs: {'PTRANS': 11, 'TRANS': 394}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 13
          Unusual residues: {' HG': 1, ' NA': 3}
          Classifications: {'peptide': 1, 'undetermined': 4}
          Modifications used: {'COO': 1, 'PEPT-D': 1}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 12
          Unusual residues: {' HG': 1, ' NA': 2}
          Classifications: {'peptide': 1, 'undetermined': 3}
          Modifications used: {'COO': 1, 'PEPT-D': 1}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 12
          Unusual residues: {' HG': 1, ' NA': 2}
          Classifications: {'peptide': 1, 'undetermined': 3}
          Modifications used: {'COO': 1, 'PEPT-D': 1}
          Link IDs: {None: 3}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1577  SG  CYS A 269      49.179  82.768  22.871  1.00 85.37           S
  ATOM   2858  SG  CYS A 441      48.431  81.437  25.785  1.00 81.69           S

  Restraints were copied for chains:
    B, C
  Time building chain proxies: 6.00, per 1000 atoms: 0.65
  Number of scatterers: 9297
  At special positions: 0
  Unit cell: (105.448, 103.296, 69.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Hg      3     79.96
     S      60     16.00
     Na      9     11.00
     O    1659      8.00
     N    1479      7.00
     C    6087      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.64
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DAS A 600 "
        pdb=" CB  DAS B 605 "
        pdb=" CB  DAS C 600 "
  Number of C-beta restraints generated:  2250

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 3 sheets defined
      85.7% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 42
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.650A  pdb=" N   ALA A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 82
      removed outlier: 4.480A  pdb=" N   LEU A  68 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
      Proline residue:  A  69  - end of helix
      removed outlier: 3.822A  pdb=" N   LEU A  82 " --> pdb=" O   GLY A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 117
      removed outlier: 3.651A  pdb=" N   GLY A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 150
      removed outlier: 3.678A  pdb=" N   ILE A 146 " --> pdb=" O   MET A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 158
    Processing helix  chain 'A' and resid 211 through 229
    Processing helix  chain 'A' and resid 230 through 232
      No H-bonds generated for 'chain 'A' and resid 230 through 232'
    Processing helix  chain 'A' and resid 233 through 273
      removed outlier: 3.590A  pdb=" N   TRP A 256 " --> pdb=" O   GLN A 252 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   TYR A 257 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      Proline residue:  A 259  - end of helix
      removed outlier: 3.599A  pdb=" N   VAL A 273 " --> pdb=" O   CYS A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 282
      removed outlier: 3.869A  pdb=" N   ARG A 280 " --> pdb=" O   TRP A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 299
    Processing helix  chain 'A' and resid 299 through 309
    Processing helix  chain 'A' and resid 312 through 320
    Processing helix  chain 'A' and resid 320 through 331
    Processing helix  chain 'A' and resid 336 through 347
    Processing helix  chain 'A' and resid 351 through 363
      removed outlier: 4.109A  pdb=" N   PHE A 357 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      Proline residue:  A 360  - end of helix
    Processing helix  chain 'A' and resid 367 through 385
    Processing helix  chain 'A' and resid 390 through 408
    Processing helix  chain 'A' and resid 413 through 418
      removed outlier: 3.581A  pdb=" N   VAL A 417 " --> pdb=" O   GLN A 413 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   THR A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 413 through 418'
    Processing helix  chain 'A' and resid 418 through 426
      removed outlier: 3.858A  pdb=" N   VAL A 422 " --> pdb=" O   THR A 418 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   VAL A 426 " --> pdb=" O   VAL A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 437
      removed outlier: 3.563A  pdb=" N   VAL A 433 " --> pdb=" O   ALA A 430 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE A 437 " --> pdb=" O   THR A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 466
      removed outlier: 3.741A  pdb=" N   LEU A 443 " --> pdb=" O   VAL A 439 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASP A 455 " --> pdb=" O   ASN A 451 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLY A 460 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 42
    Processing helix  chain 'B' and resid 45 through 53
      removed outlier: 3.651A  pdb=" N   ALA B  53 " --> pdb=" O   LYS B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 82
      removed outlier: 4.480A  pdb=" N   LEU B  68 " --> pdb=" O   LYS B  64 " (cutoff:3.500A)
      Proline residue:  B  69  - end of helix
      removed outlier: 3.822A  pdb=" N   LEU B  82 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 117
      removed outlier: 3.650A  pdb=" N   GLY B  91 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 150
      removed outlier: 3.679A  pdb=" N   ILE B 146 " --> pdb=" O   MET B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 158
    Processing helix  chain 'B' and resid 211 through 229
    Processing helix  chain 'B' and resid 230 through 232
      No H-bonds generated for 'chain 'B' and resid 230 through 232'
    Processing helix  chain 'B' and resid 233 through 273
      removed outlier: 3.589A  pdb=" N   TRP B 256 " --> pdb=" O   GLN B 252 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   TYR B 257 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
      Proline residue:  B 259  - end of helix
      removed outlier: 3.599A  pdb=" N   VAL B 273 " --> pdb=" O   CYS B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 282
      removed outlier: 3.869A  pdb=" N   ARG B 280 " --> pdb=" O   TRP B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 299
    Processing helix  chain 'B' and resid 299 through 309
    Processing helix  chain 'B' and resid 312 through 320
    Processing helix  chain 'B' and resid 320 through 331
    Processing helix  chain 'B' and resid 336 through 347
    Processing helix  chain 'B' and resid 351 through 363
      removed outlier: 4.108A  pdb=" N   PHE B 357 " --> pdb=" O   ARG B 353 " (cutoff:3.500A)
      Proline residue:  B 360  - end of helix
    Processing helix  chain 'B' and resid 367 through 385
    Processing helix  chain 'B' and resid 390 through 408
    Processing helix  chain 'B' and resid 413 through 418
      removed outlier: 3.581A  pdb=" N   VAL B 417 " --> pdb=" O   GLN B 413 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   THR B 418 " --> pdb=" O   ALA B 414 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 413 through 418'
    Processing helix  chain 'B' and resid 418 through 426
      removed outlier: 3.859A  pdb=" N   VAL B 422 " --> pdb=" O   THR B 418 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   VAL B 426 " --> pdb=" O   VAL B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 437
      removed outlier: 3.563A  pdb=" N   VAL B 433 " --> pdb=" O   ALA B 430 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE B 437 " --> pdb=" O   THR B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 466
      removed outlier: 3.741A  pdb=" N   LEU B 443 " --> pdb=" O   VAL B 439 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASP B 455 " --> pdb=" O   ASN B 451 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLY B 460 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 42
    Processing helix  chain 'C' and resid 45 through 53
      removed outlier: 3.650A  pdb=" N   ALA C  53 " --> pdb=" O   LYS C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 82
      removed outlier: 4.480A  pdb=" N   LEU C  68 " --> pdb=" O   LYS C  64 " (cutoff:3.500A)
      Proline residue:  C  69  - end of helix
      removed outlier: 3.821A  pdb=" N   LEU C  82 " --> pdb=" O   GLY C  78 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 117
      removed outlier: 3.651A  pdb=" N   GLY C  91 " --> pdb=" O   SER C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 150
      removed outlier: 3.678A  pdb=" N   ILE C 146 " --> pdb=" O   MET C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 158
    Processing helix  chain 'C' and resid 211 through 229
    Processing helix  chain 'C' and resid 230 through 232
      No H-bonds generated for 'chain 'C' and resid 230 through 232'
    Processing helix  chain 'C' and resid 233 through 273
      removed outlier: 3.590A  pdb=" N   TRP C 256 " --> pdb=" O   GLN C 252 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   TYR C 257 " --> pdb=" O   ILE C 253 " (cutoff:3.500A)
      Proline residue:  C 259  - end of helix
      removed outlier: 3.599A  pdb=" N   VAL C 273 " --> pdb=" O   CYS C 269 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 276 through 282
      removed outlier: 3.869A  pdb=" N   ARG C 280 " --> pdb=" O   TRP C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 299
    Processing helix  chain 'C' and resid 299 through 309
    Processing helix  chain 'C' and resid 312 through 320
    Processing helix  chain 'C' and resid 320 through 331
    Processing helix  chain 'C' and resid 336 through 347
    Processing helix  chain 'C' and resid 351 through 363
      removed outlier: 4.108A  pdb=" N   PHE C 357 " --> pdb=" O   ARG C 353 " (cutoff:3.500A)
      Proline residue:  C 360  - end of helix
    Processing helix  chain 'C' and resid 367 through 385
    Processing helix  chain 'C' and resid 390 through 408
    Processing helix  chain 'C' and resid 413 through 418
      removed outlier: 3.581A  pdb=" N   VAL C 417 " --> pdb=" O   GLN C 413 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   THR C 418 " --> pdb=" O   ALA C 414 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 413 through 418'
    Processing helix  chain 'C' and resid 418 through 426
      removed outlier: 3.859A  pdb=" N   VAL C 422 " --> pdb=" O   THR C 418 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   VAL C 426 " --> pdb=" O   VAL C 422 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 437
      removed outlier: 3.563A  pdb=" N   VAL C 433 " --> pdb=" O   ALA C 430 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE C 437 " --> pdb=" O   THR C 434 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 466
      removed outlier: 3.741A  pdb=" N   LEU C 443 " --> pdb=" O   VAL C 439 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASP C 455 " --> pdb=" O   ASN C 451 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLY C 460 " --> pdb=" O   ALA C 456 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167
    Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167
    Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167

    726 hydrogen bonds defined for protein.
    2133 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.01

  Time building geometry restraints manager: 2.98 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1788
        1.33 -     1.45: 1951
        1.45 -     1.57: 5567
        1.57 -     1.69: 0
        1.69 -     1.81: 111
  Bond restraints: 9417
  Sorted by residual:
  bond pdb=" N   VAL C 417 "
       pdb=" CA  VAL C 417 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.038 1.21e-02 6.83e+03 9.80e+00
  bond pdb=" N   VAL A 417 "
       pdb=" CA  VAL A 417 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 1.21e-02 6.83e+03 9.34e+00
  bond pdb=" N   VAL B 417 "
       pdb=" CA  VAL B 417 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.037 1.21e-02 6.83e+03 9.28e+00
  bond pdb=" N   LEU C 328 "
       pdb=" CA  LEU C 328 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.35e-02 5.49e+03 5.57e+00
  bond pdb=" N   ARG A 445 "
       pdb=" CA  ARG A 445 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.45e+00
  ... (remaining 9412 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 12180
        1.26 -     2.52: 459
        2.52 -     3.78: 112
        3.78 -     5.04: 29
        5.04 -     6.29: 3
  Bond angle restraints: 12783
  Sorted by residual:
  angle pdb=" CA  PRO A 412 "
        pdb=" C   PRO A 412 "
        pdb=" O   PRO A 412 "
      ideal   model   delta    sigma   weight residual
     121.23  117.53    3.70 1.07e+00 8.73e-01 1.19e+01
  angle pdb=" CA  PRO C 412 "
        pdb=" C   PRO C 412 "
        pdb=" O   PRO C 412 "
      ideal   model   delta    sigma   weight residual
     121.23  117.53    3.70 1.07e+00 8.73e-01 1.19e+01
  angle pdb=" CA  PRO B 412 "
        pdb=" C   PRO B 412 "
        pdb=" O   PRO B 412 "
      ideal   model   delta    sigma   weight residual
     121.23  117.56    3.67 1.07e+00 8.73e-01 1.18e+01
  angle pdb=" CA  VAL A 417 "
        pdb=" C   VAL A 417 "
        pdb=" O   VAL A 417 "
      ideal   model   delta    sigma   weight residual
     120.85  117.88    2.97 1.06e+00 8.90e-01 7.87e+00
  angle pdb=" CA  VAL C 417 "
        pdb=" C   VAL C 417 "
        pdb=" O   VAL C 417 "
      ideal   model   delta    sigma   weight residual
     120.85  117.88    2.97 1.06e+00 8.90e-01 7.86e+00
  ... (remaining 12778 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.63: 5238
       25.63 -    51.26: 330
       51.26 -    76.90: 42
       76.90 -   102.53: 3
      102.53 -   128.16: 3
  Dihedral angle restraints: 5616
    sinusoidal: 2127
      harmonic: 3489
  Sorted by residual:
  dihedral pdb=" CA  DAS B 605 "
           pdb=" CB  DAS B 605 "
           pdb=" CG  DAS B 605 "
           pdb=" OD1 DAS B 605 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00 -158.16  128.16     1      2.00e+01 2.50e-03 3.88e+01
  dihedral pdb=" CA  DAS A 600 "
           pdb=" CB  DAS A 600 "
           pdb=" CG  DAS A 600 "
           pdb=" OD1 DAS A 600 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00 -158.16  128.16     1      2.00e+01 2.50e-03 3.88e+01
  dihedral pdb=" CA  DAS C 600 "
           pdb=" CB  DAS C 600 "
           pdb=" CG  DAS C 600 "
           pdb=" OD1 DAS C 600 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00 -158.14  128.14     1      2.00e+01 2.50e-03 3.88e+01
  ... (remaining 5613 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1191
       0.040 -    0.080: 354
       0.080 -    0.120: 69
       0.120 -    0.160: 9
       0.160 -    0.200: 3
  Chirality restraints: 1626
  Sorted by residual:
  chirality pdb=" CA  MET B 367 "
            pdb=" N   MET B 367 "
            pdb=" C   MET B 367 "
            pdb=" CB  MET B 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.99e-01
  chirality pdb=" CA  MET A 367 "
            pdb=" N   MET A 367 "
            pdb=" C   MET A 367 "
            pdb=" CB  MET A 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.94e-01
  chirality pdb=" CA  MET C 367 "
            pdb=" N   MET C 367 "
            pdb=" C   MET C 367 "
            pdb=" CB  MET C 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.80e-01
  ... (remaining 1623 not shown)

  Planarity restraints: 1557
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 166 "   -0.250 9.50e-02 1.11e+02   1.13e-01 9.43e+00
        pdb=" NE  ARG A 166 "    0.022 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 166 "   -0.020 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 166 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 166 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 166 "    0.250 9.50e-02 1.11e+02   1.13e-01 9.42e+00
        pdb=" NE  ARG C 166 "   -0.022 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 166 "    0.020 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 166 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 166 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 166 "    0.250 9.50e-02 1.11e+02   1.13e-01 9.35e+00
        pdb=" NE  ARG B 166 "   -0.022 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 166 "    0.019 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 166 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 166 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1554 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 221
        2.69 -     3.25: 10163
        3.25 -     3.80: 15569
        3.80 -     4.35: 20822
        4.35 -     4.90: 34232
  Nonbonded interactions: 81007
  Sorted by model distance:
  nonbonded pdb=" O   THR A 364 "
            pdb="NA    NA A 602 "
     model   vdw
     2.143 2.470
  nonbonded pdb=" O   THR B 364 "
            pdb="NA    NA B 603 "
     model   vdw
     2.143 2.470
  nonbonded pdb=" O   THR C 364 "
            pdb="NA    NA C 602 "
     model   vdw
     2.143 2.470
  nonbonded pdb=" O   ALA A 408 "
            pdb="NA    NA A 602 "
     model   vdw
     2.161 2.470
  nonbonded pdb=" O   ALA B 408 "
            pdb="NA    NA B 603 "
     model   vdw
     2.161 2.470
  ... (remaining 81002 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: 0.06
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 17 through 470 or resid 601 through 603))
  selection = (chain 'B' and (resid 17 through 470 or resid 602 through 604))
  selection = (chain 'C' and (resid 17 through 470 or resid 601 through 603))
}

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:             0.760
  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:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.220
  Find NCS groups from input model:        0.480
  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:12.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
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      :  0.003   0.038   9417  Z= 0.215
  Angle     :  0.605   6.295  12783  Z= 0.326
  Chirality :  0.040   0.200   1626
  Planarity :  0.007   0.113   1557
  Dihedral  : 16.101 128.161   3366
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 22.55 %
    Favored  : 77.45 %
  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:  0.93 (0.24), residues: 1200
  helix:  1.15 (0.17), residues: 924
  sheet: -0.46 (0.66), residues: 54
  loop : -1.11 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 256 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.016   0.002   PHE C 240 
 TYR   0.014   0.001   TYR B  97 
 ARG   0.023   0.002   ARG C 166 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 PHE cc_start: 0.7113 (t80) cc_final: 0.6592 (t80)
REVERT: A  103 LEU cc_start: 0.7427 (mm) cc_final: 0.7209 (mm)
REVERT: A  117 LYS cc_start: 0.7594 (mtmm) cc_final: 0.6834 (mttp)
REVERT: A  142 MET cc_start: 0.8083 (tpp) cc_final: 0.7764 (mmp)
REVERT: A  205 MET cc_start: 0.7813 (ptt) cc_final: 0.7247 (pmm)
REVERT: A  207 SER cc_start: 0.7809 (p) cc_final: 0.7498 (m)
REVERT: A  255 MET cc_start: 0.8217 (tpp) cc_final: 0.7881 (mmm)
REVERT: A  258 MET cc_start: 0.7963 (tpp) cc_final: 0.7721 (ttt)
REVERT: A  315 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.6987 (ttm110)
REVERT: A  352 LYS cc_start: 0.6843 (mttp) cc_final: 0.6619 (mtmm)
REVERT: B  205 MET cc_start: 0.8009 (ptt) cc_final: 0.7295 (pmm)
REVERT: B  255 MET cc_start: 0.8249 (tpp) cc_final: 0.7857 (mmm)
REVERT: B  258 MET cc_start: 0.8131 (tpp) cc_final: 0.7918 (ttt)
REVERT: B  277 GLU cc_start: 0.6747 (mt-10) cc_final: 0.6502 (mp0)
REVERT: B  315 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.6999 (ttm170)
REVERT: B  352 LYS cc_start: 0.6964 (mttp) cc_final: 0.6732 (mtmm)
REVERT: B  356 ARG cc_start: 0.6903 (mmt180) cc_final: 0.6558 (mmt180)
REVERT: B  399 ILE cc_start: 0.8138 (mm) cc_final: 0.7898 (mt)
REVERT: C   60 MET cc_start: 0.8451 (mmm) cc_final: 0.8251 (mmm)
REVERT: C   99 PHE cc_start: 0.7593 (t80) cc_final: 0.7392 (t80)
REVERT: C  138 THR cc_start: 0.6518 (t) cc_final: 0.6176 (m)
REVERT: C  205 MET cc_start: 0.7997 (ptt) cc_final: 0.7545 (ptm)
REVERT: C  241 ASN cc_start: 0.8351 (t0) cc_final: 0.8062 (m-40)
REVERT: C  315 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.7067 (ttm110)
REVERT: C  318 MET cc_start: 0.6261 (tpt) cc_final: 0.6035 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 1.2346
  time to fit residues: 293.6091
Evaluate side-chains
  169 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 90 optimal weight:    7.9990
   chunk 50 optimal weight:    7.9990
   chunk 31 optimal weight:    0.5980
   chunk 61 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 94 optimal weight:    0.8980
   chunk 36 optimal weight:    0.1980
   chunk 57 optimal weight:    0.5980
   chunk 70 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9990
   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 322 GLN
A 347 ASN
B 322 GLN
B 347 ASN
C 322 GLN
C 347 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.185192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.149141 restraints weight = 2974.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 0.67
r_work: 0.3309 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 2.61 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9417  Z= 0.212
  Angle     :  0.533   5.136  12783  Z= 0.278
  Chirality :  0.039   0.150   1626
  Planarity :  0.004   0.027   1557
  Dihedral  :  6.601 103.084   1287
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 22.06 %
    Favored  : 75.57 %
  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:  1.53 (0.23), residues: 1200
  helix:  1.56 (0.16), residues: 915
  sheet:  0.19 (0.60), residues: 48
  loop : -0.83 (0.42), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 256 
 HIS   0.002   0.001   HIS B 296 
 PHE   0.013   0.002   PHE C 240 
 TYR   0.011   0.001   TYR C  97 
 ARG   0.002   0.000   ARG C 166 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 187
  time to evaluate  : 1.037 
Fit side-chains
REVERT: A   99 PHE cc_start: 0.7906 (t80) cc_final: 0.7583 (t80)
REVERT: A  117 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7614 (mttp)
REVERT: A  315 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7255 (ttm110)
REVERT: A  353 ARG cc_start: 0.7897 (mtm180) cc_final: 0.7637 (mtm-85)
REVERT: A  442 LEU cc_start: 0.7546 (tp) cc_final: 0.7307 (tt)
REVERT: A  444 ASP cc_start: 0.8004 (t0) cc_final: 0.7776 (t0)
REVERT: B   68 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7403 (tp)
REVERT: B  205 MET cc_start: 0.8333 (ptt) cc_final: 0.8114 (ptm)
REVERT: B  258 MET cc_start: 0.8443 (tpp) cc_final: 0.8036 (tpt)
REVERT: B  277 GLU cc_start: 0.6782 (mt-10) cc_final: 0.6480 (mp0)
REVERT: B  304 ILE cc_start: 0.7787 (tt) cc_final: 0.7476 (mt)
REVERT: B  315 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7316 (ttm170)
REVERT: C   68 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7405 (tp)
REVERT: C  138 THR cc_start: 0.6974 (t) cc_final: 0.6586 (m)
REVERT: C  205 MET cc_start: 0.8332 (ptt) cc_final: 0.8047 (ptm)
REVERT: C  228 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7699 (mmtm)
REVERT: C  315 ARG cc_start: 0.8056 (ttm-80) cc_final: 0.7377 (ttm110)
REVERT: C  442 LEU cc_start: 0.7595 (tp) cc_final: 0.7380 (tt)
REVERT: C  444 ASP cc_start: 0.8197 (t0) cc_final: 0.7855 (t70)
  outliers start: 24
  outliers final: 4
  residues processed: 199
  average time/residue: 1.1585
  time to fit residues: 247.5117
Evaluate side-chains
  172 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 166
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain C residue   66 ILE
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  229 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 2 optimal weight:    0.0770
   chunk 92 optimal weight:    1.9990
   chunk 91 optimal weight:    0.5980
   chunk 84 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    0.1980
   chunk 85 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 104 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.4538

-------------------------------------------------------------------------------
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 = 0.4024 r_free = 0.4024 target = 0.188512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.154462 restraints weight = 2595.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 0.60
r_work: 0.3377 rms_B_bonded: 1.40 restraints_weight: 0.5000
r_work: 0.3253 rms_B_bonded: 2.22 restraints_weight: 0.2500
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9417  Z= 0.184
  Angle     :  0.495   5.141  12783  Z= 0.256
  Chirality :  0.038   0.138   1626
  Planarity :  0.003   0.029   1557
  Dihedral  :  6.258  88.089   1287
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 21.36 %
    Favored  : 74.68 %
  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:  1.55 (0.23), residues: 1200
  helix:  1.59 (0.16), residues: 933
  sheet:  0.10 (0.60), residues: 48
  loop : -1.12 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 256 
 HIS   0.002   0.001   HIS B 296 
 PHE   0.012   0.001   PHE C 240 
 TYR   0.009   0.001   TYR A 162 
 ARG   0.001   0.000   ARG B 315 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 185
  time to evaluate  : 1.015 
Fit side-chains
REVERT: A   99 PHE cc_start: 0.7940 (t80) cc_final: 0.7588 (t80)
REVERT: A  117 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7663 (mttp)
REVERT: A  138 THR cc_start: 0.7074 (OUTLIER) cc_final: 0.6701 (m)
REVERT: A  277 GLU cc_start: 0.6535 (tm-30) cc_final: 0.5984 (pm20)
REVERT: A  303 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7684 (tp)
REVERT: A  315 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7317 (ttm110)
REVERT: A  320 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7957 (mtp)
REVERT: A  353 ARG cc_start: 0.7933 (mtm180) cc_final: 0.7713 (mtm-85)
REVERT: A  356 ARG cc_start: 0.7025 (mmt180) cc_final: 0.6775 (mmt180)
REVERT: A  444 ASP cc_start: 0.7984 (t0) cc_final: 0.7717 (t0)
REVERT: B   48 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7720 (mp0)
REVERT: B   68 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7388 (tp)
REVERT: B  138 THR cc_start: 0.6968 (OUTLIER) cc_final: 0.6629 (m)
REVERT: B  167 GLU cc_start: 0.7735 (pp20) cc_final: 0.7441 (pp20)
REVERT: B  228 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7630 (mmtm)
REVERT: B  258 MET cc_start: 0.8463 (tpp) cc_final: 0.8110 (tpt)
REVERT: B  272 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7047 (mp0)
REVERT: B  277 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6486 (mp0)
REVERT: B  303 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7586 (tt)
REVERT: B  304 ILE cc_start: 0.7803 (tt) cc_final: 0.7584 (mt)
REVERT: B  315 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7400 (ttm170)
REVERT: B  445 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.6976 (mtt90)
REVERT: C   68 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7384 (tp)
REVERT: C  138 THR cc_start: 0.7112 (OUTLIER) cc_final: 0.6707 (m)
REVERT: C  163 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8026 (ptpt)
REVERT: C  205 MET cc_start: 0.8146 (ptt) cc_final: 0.7880 (ptm)
REVERT: C  228 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7520 (mtmt)
REVERT: C  304 ILE cc_start: 0.7977 (tt) cc_final: 0.7670 (mt)
REVERT: C  315 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7492 (ttm110)
REVERT: C  442 LEU cc_start: 0.7352 (tp) cc_final: 0.7152 (tt)
REVERT: C  444 ASP cc_start: 0.8060 (t0) cc_final: 0.7762 (t70)
  outliers start: 40
  outliers final: 11
  residues processed: 213
  average time/residue: 1.2227
  time to fit residues: 278.5405
Evaluate side-chains
  185 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 164
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  235 ILE
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  445 ARG
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  163 LYS
Chi-restraints excluded: chain C residue  202 ILE
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  269 CYS
Chi-restraints excluded: chain C residue  437 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0980
   chunk 10 optimal weight:    0.5980
   chunk 104 optimal weight:    0.3980
   chunk 18 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0670
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
B 241 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.199330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.164098 restraints weight = 2895.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 0.71
r_work: 0.3655 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3544 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9417  Z= 0.169
  Angle     :  0.483   5.135  12783  Z= 0.250
  Chirality :  0.038   0.134   1626
  Planarity :  0.003   0.030   1557
  Dihedral  :  5.980  77.919   1287
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 22.75 %
    Favored  : 74.09 %
  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:  1.67 (0.23), residues: 1200
  helix:  1.68 (0.16), residues: 933
  sheet:  0.07 (0.62), residues: 48
  loop : -1.05 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 256 
 HIS   0.001   0.001   HIS B 296 
 PHE   0.011   0.001   PHE B 240 
 TYR   0.009   0.001   TYR B 162 
 ARG   0.002   0.000   ARG A 445 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 172
  time to evaluate  : 1.074 
Fit side-chains
REVERT: A   99 PHE cc_start: 0.7941 (t80) cc_final: 0.7495 (t80)
REVERT: A  117 LYS cc_start: 0.8225 (mtmm) cc_final: 0.7633 (mttp)
REVERT: A  138 THR cc_start: 0.6937 (OUTLIER) cc_final: 0.6575 (m)
REVERT: A  277 GLU cc_start: 0.6262 (tm-30) cc_final: 0.6015 (mp0)
REVERT: A  303 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7626 (tp)
REVERT: A  315 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7241 (ttm110)
REVERT: A  342 ARG cc_start: 0.7422 (ttm170) cc_final: 0.7216 (ttm110)
REVERT: A  353 ARG cc_start: 0.7903 (mtm180) cc_final: 0.7683 (mtm-85)
REVERT: A  356 ARG cc_start: 0.6999 (mmt180) cc_final: 0.6681 (mmt180)
REVERT: A  444 ASP cc_start: 0.7965 (t0) cc_final: 0.7705 (t70)
REVERT: B   68 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7337 (tp)
REVERT: B   99 PHE cc_start: 0.8058 (t80) cc_final: 0.7776 (t80)
REVERT: B  138 THR cc_start: 0.6904 (OUTLIER) cc_final: 0.6580 (m)
REVERT: B  228 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7542 (mmtm)
REVERT: B  258 MET cc_start: 0.8493 (tpp) cc_final: 0.8176 (tpt)
REVERT: B  277 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6508 (mp0)
REVERT: B  303 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7588 (tt)
REVERT: B  315 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7327 (ttm170)
REVERT: B  445 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6981 (mtt90)
REVERT: C   40 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7019 (mt-10)
REVERT: C   68 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7288 (tp)
REVERT: C  138 THR cc_start: 0.7001 (OUTLIER) cc_final: 0.6568 (m)
REVERT: C  163 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.7913 (ptpt)
REVERT: C  205 MET cc_start: 0.8129 (ptt) cc_final: 0.7816 (ptm)
REVERT: C  228 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7526 (mmtm)
REVERT: C  235 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7981 (tt)
REVERT: C  304 ILE cc_start: 0.7782 (tt) cc_final: 0.7469 (mt)
REVERT: C  315 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7400 (ttm110)
REVERT: C  419 MET cc_start: 0.8763 (mmm) cc_final: 0.8463 (tpp)
REVERT: C  444 ASP cc_start: 0.8075 (t0) cc_final: 0.7774 (t70)
  outliers start: 32
  outliers final: 11
  residues processed: 190
  average time/residue: 1.1630
  time to fit residues: 237.1978
Evaluate side-chains
  184 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 163
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  235 ILE
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  445 ARG
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  163 LYS
Chi-restraints excluded: chain C residue  235 ILE
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  269 CYS
Chi-restraints excluded: chain C residue  437 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0870
   chunk 103 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 87 optimal weight:    0.1980
   chunk 41 optimal weight:    0.0270
   chunk 113 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0980
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.2216

-------------------------------------------------------------------------------
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 = 0.4185 r_free = 0.4185 target = 0.200955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.165400 restraints weight = 2676.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 0.71
r_work: 0.3702 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3593 rms_B_bonded: 2.62 restraints_weight: 0.2500
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9417  Z= 0.145
  Angle     :  0.463   5.742  12783  Z= 0.239
  Chirality :  0.037   0.129   1626
  Planarity :  0.003   0.031   1557
  Dihedral  :  4.757  63.105   1287
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 24.13 %
    Favored  : 72.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.23), residues: 1200
  helix:  1.80 (0.16), residues: 924
  sheet:  0.03 (0.62), residues: 48
  loop : -0.66 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 256 
 HIS   0.001   0.000   HIS B 296 
 PHE   0.008   0.001   PHE C 240 
 TYR   0.010   0.001   TYR A 162 
 ARG   0.001   0.000   ARG A  39 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 182
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A   99 PHE cc_start: 0.7853 (t80) cc_final: 0.7397 (t80)
REVERT: A  117 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7531 (mttp)
REVERT: A  138 THR cc_start: 0.6798 (OUTLIER) cc_final: 0.6401 (m)
REVERT: A  303 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7578 (tp)
REVERT: A  315 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7186 (ttm110)
REVERT: A  356 ARG cc_start: 0.7019 (mmt180) cc_final: 0.6707 (mmt180)
REVERT: A  444 ASP cc_start: 0.7798 (t0) cc_final: 0.7302 (t70)
REVERT: B   48 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7684 (mp0)
REVERT: B   68 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7334 (tp)
REVERT: B   99 PHE cc_start: 0.7909 (t80) cc_final: 0.7637 (t80)
REVERT: B  138 THR cc_start: 0.6789 (OUTLIER) cc_final: 0.6540 (m)
REVERT: B  167 GLU cc_start: 0.7790 (pp20) cc_final: 0.7386 (pp20)
REVERT: B  228 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7332 (mmtm)
REVERT: B  258 MET cc_start: 0.8399 (tpp) cc_final: 0.8122 (tpt)
REVERT: B  272 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6781 (mp0)
REVERT: B  277 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6455 (mp0)
REVERT: B  303 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7479 (mt)
REVERT: B  315 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7280 (ttm170)
REVERT: B  353 ARG cc_start: 0.7691 (mpp-170) cc_final: 0.7474 (mpp-170)
REVERT: C   68 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7235 (tp)
REVERT: C  138 THR cc_start: 0.6611 (OUTLIER) cc_final: 0.6289 (m)
REVERT: C  167 GLU cc_start: 0.7270 (pp20) cc_final: 0.7022 (pp20)
REVERT: C  205 MET cc_start: 0.8057 (ptt) cc_final: 0.7735 (ptm)
REVERT: C  228 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7406 (mmtm)
REVERT: C  235 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7804 (tt)
REVERT: C  277 GLU cc_start: 0.6242 (tm-30) cc_final: 0.6018 (pm20)
REVERT: C  304 ILE cc_start: 0.7754 (tt) cc_final: 0.7447 (mt)
REVERT: C  315 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7388 (ttm110)
REVERT: C  419 MET cc_start: 0.8766 (mmm) cc_final: 0.8354 (tpp)
REVERT: C  444 ASP cc_start: 0.7920 (t0) cc_final: 0.7623 (t70)
  outliers start: 30
  outliers final: 9
  residues processed: 201
  average time/residue: 1.2233
  time to fit residues: 263.7674
Evaluate side-chains
  185 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 1.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  235 ILE
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  235 ILE
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  269 CYS
Chi-restraints excluded: chain C residue  437 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 74 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 23 optimal weight:    0.4980
   chunk 58 optimal weight:    1.9990
   chunk 104 optimal weight:    4.9990
   chunk 11 optimal weight:    0.5980
   chunk 84 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.4139 r_free = 0.4139 target = 0.195927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.161736 restraints weight = 2386.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 0.63
r_work: 0.3626 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3514 rms_B_bonded: 2.47 restraints_weight: 0.2500
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9417  Z= 0.262
  Angle     :  0.535   5.666  12783  Z= 0.275
  Chirality :  0.040   0.135   1626
  Planarity :  0.004   0.033   1557
  Dihedral  :  4.426  50.503   1287
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 22.65 %
    Favored  : 73.19 %
  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:  1.50 (0.23), residues: 1200
  helix:  1.53 (0.16), residues: 939
  sheet:  0.00 (0.63), residues: 48
  loop : -1.05 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 256 
 HIS   0.003   0.001   HIS C 296 
 PHE   0.018   0.002   PHE C 240 
 TYR   0.010   0.001   TYR A 162 
 ARG   0.002   0.000   ARG C 353 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 159
  time to evaluate  : 1.006 
Fit side-chains
REVERT: A   99 PHE cc_start: 0.7995 (t80) cc_final: 0.7538 (t80)
REVERT: A  117 LYS cc_start: 0.8264 (mtmm) cc_final: 0.7677 (mttp)
REVERT: A  138 THR cc_start: 0.6891 (OUTLIER) cc_final: 0.6508 (m)
REVERT: A  303 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7688 (tp)
REVERT: A  315 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7346 (ttm110)
REVERT: A  356 ARG cc_start: 0.6998 (mmt180) cc_final: 0.6697 (mmt180)
REVERT: A  444 ASP cc_start: 0.7996 (t0) cc_final: 0.7722 (t70)
REVERT: B   68 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7330 (tp)
REVERT: B  138 THR cc_start: 0.6962 (OUTLIER) cc_final: 0.6723 (m)
REVERT: B  258 MET cc_start: 0.8408 (tpp) cc_final: 0.8143 (tpt)
REVERT: B  277 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6358 (pm20)
REVERT: B  315 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7365 (ttm170)
REVERT: B  445 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.6862 (mtt90)
REVERT: C   68 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7288 (tp)
REVERT: C  117 LYS cc_start: 0.8297 (mtmm) cc_final: 0.6604 (tmtt)
REVERT: C  138 THR cc_start: 0.6856 (OUTLIER) cc_final: 0.6546 (m)
REVERT: C  205 MET cc_start: 0.8201 (ptt) cc_final: 0.7959 (ptm)
REVERT: C  228 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7557 (mtmt)
REVERT: C  277 GLU cc_start: 0.6463 (tm-30) cc_final: 0.6201 (pm20)
REVERT: C  304 ILE cc_start: 0.7832 (tt) cc_final: 0.7583 (mt)
REVERT: C  315 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7419 (ttm110)
REVERT: C  419 MET cc_start: 0.8881 (mmm) cc_final: 0.8590 (tpp)
REVERT: C  444 ASP cc_start: 0.8080 (t0) cc_final: 0.7862 (t70)
  outliers start: 42
  outliers final: 11
  residues processed: 186
  average time/residue: 1.1657
  time to fit residues: 232.5903
Evaluate side-chains
  180 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 162
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  235 ILE
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  445 ARG
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   66 ILE
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  269 CYS
Chi-restraints excluded: chain C residue  309 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 56 optimal weight:    0.0670
   chunk 93 optimal weight:    0.8980
   chunk 101 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 97 optimal weight:    0.5980
   chunk 103 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0970
   chunk 50 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.4716

-------------------------------------------------------------------------------
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 = 0.4162 r_free = 0.4162 target = 0.198351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.164085 restraints weight = 2411.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3829 rms_B_bonded: 0.65
r_work: 0.3655 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3541 rms_B_bonded: 2.50 restraints_weight: 0.2500
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9417  Z= 0.180
  Angle     :  0.488   5.181  12783  Z= 0.251
  Chirality :  0.038   0.149   1626
  Planarity :  0.004   0.034   1557
  Dihedral  :  3.839  34.862   1287
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 23.24 %
    Favored  : 73.49 %
  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:  1.68 (0.23), residues: 1200
  helix:  1.71 (0.16), residues: 924
  sheet: -0.23 (0.64), residues: 48
  loop : -0.98 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 256 
 HIS   0.001   0.000   HIS B 296 
 PHE   0.012   0.001   PHE C 240 
 TYR   0.010   0.001   TYR B 162 
 ARG   0.006   0.000   ARG A 353 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 170
  time to evaluate  : 1.003 
Fit side-chains
REVERT: A   75 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8013 (mmt)
REVERT: A   99 PHE cc_start: 0.7917 (t80) cc_final: 0.7436 (t80)
REVERT: A  117 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7624 (mttp)
REVERT: A  167 GLU cc_start: 0.7456 (pp20) cc_final: 0.7019 (pp20)
REVERT: A  303 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7469 (tp)
REVERT: A  315 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7241 (ttm110)
REVERT: A  356 ARG cc_start: 0.7036 (mmt180) cc_final: 0.6722 (mmt180)
REVERT: A  444 ASP cc_start: 0.7860 (t0) cc_final: 0.7551 (t70)
REVERT: B   48 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7641 (mp0)
REVERT: B   68 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7291 (tp)
REVERT: B   99 PHE cc_start: 0.7991 (t80) cc_final: 0.7691 (t80)
REVERT: B  114 VAL cc_start: 0.7983 (t) cc_final: 0.7747 (m)
REVERT: B  138 THR cc_start: 0.6865 (OUTLIER) cc_final: 0.6600 (m)
REVERT: B  167 GLU cc_start: 0.7774 (pp20) cc_final: 0.7425 (pp20)
REVERT: B  258 MET cc_start: 0.8398 (tpp) cc_final: 0.8120 (tpt)
REVERT: B  277 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6402 (pm20)
REVERT: B  315 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7300 (ttm170)
REVERT: B  440 ASP cc_start: 0.7539 (t70) cc_final: 0.7229 (t0)
REVERT: B  445 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7383 (mmt180)
REVERT: C   68 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7218 (tp)
REVERT: C  114 VAL cc_start: 0.8173 (t) cc_final: 0.7888 (m)
REVERT: C  117 LYS cc_start: 0.8294 (mtmm) cc_final: 0.6589 (tmtt)
REVERT: C  205 MET cc_start: 0.8153 (ptt) cc_final: 0.7835 (ptm)
REVERT: C  228 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7524 (mmtm)
REVERT: C  304 ILE cc_start: 0.7774 (tt) cc_final: 0.7468 (mt)
REVERT: C  315 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7391 (ttm110)
REVERT: C  419 MET cc_start: 0.8873 (mmm) cc_final: 0.8554 (tpp)
REVERT: C  442 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6903 (tt)
REVERT: C  444 ASP cc_start: 0.7970 (t0) cc_final: 0.7695 (t70)
  outliers start: 33
  outliers final: 8
  residues processed: 190
  average time/residue: 1.1786
  time to fit residues: 239.8312
Evaluate side-chains
  169 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 154
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  235 ILE
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  445 ARG
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  269 CYS
Chi-restraints excluded: chain C residue  309 VAL
Chi-restraints excluded: chain C residue  442 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 116 optimal weight:    0.0870
   chunk 15 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 74 optimal weight:    0.4980
   chunk 57 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0980
   overall best weight:    0.3958

-------------------------------------------------------------------------------
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 = 0.4077 r_free = 0.4077 target = 0.192558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.161759 restraints weight = 2243.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 0.50
r_work: 0.3587 rms_B_bonded: 1.45 restraints_weight: 0.5000
r_work: 0.3461 rms_B_bonded: 2.31 restraints_weight: 0.2500
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9417  Z= 0.174
  Angle     :  0.498   5.301  12783  Z= 0.256
  Chirality :  0.038   0.144   1626
  Planarity :  0.004   0.033   1557
  Dihedral  :  3.737  33.864   1287
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 24.23 %
    Favored  : 73.00 %
  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:  1.78 (0.23), residues: 1200
  helix:  1.80 (0.16), residues: 906
  sheet: -0.23 (0.65), residues: 48
  loop : -0.79 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 256 
 HIS   0.001   0.000   HIS B 296 
 PHE   0.012   0.001   PHE C 240 
 TYR   0.011   0.001   TYR B 162 
 ARG   0.006   0.000   ARG A 353 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 160
  time to evaluate  : 1.015 
Fit side-chains
REVERT: A   99 PHE cc_start: 0.7962 (t80) cc_final: 0.7565 (t80)
REVERT: A  117 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7656 (mttp)
REVERT: A  167 GLU cc_start: 0.7381 (pp20) cc_final: 0.7019 (pp20)
REVERT: A  303 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7758 (tp)
REVERT: A  315 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7379 (ttm170)
REVERT: A  342 ARG cc_start: 0.7423 (ttm110) cc_final: 0.7191 (ttm110)
REVERT: A  356 ARG cc_start: 0.7083 (mmt180) cc_final: 0.6834 (mmt180)
REVERT: A  444 ASP cc_start: 0.7827 (t0) cc_final: 0.7521 (t70)
REVERT: B   68 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7478 (tp)
REVERT: B   99 PHE cc_start: 0.8024 (t80) cc_final: 0.7762 (t80)
REVERT: B  258 MET cc_start: 0.8373 (tpp) cc_final: 0.8084 (tpt)
REVERT: B  277 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6445 (pm20)
REVERT: B  315 ARG cc_start: 0.7888 (ttm-80) cc_final: 0.7342 (ttm170)
REVERT: B  440 ASP cc_start: 0.7718 (t70) cc_final: 0.7425 (t0)
REVERT: B  445 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7422 (mmt180)
REVERT: C   68 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7279 (tp)
REVERT: C  205 MET cc_start: 0.8171 (ptt) cc_final: 0.7869 (ptm)
REVERT: C  228 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7620 (mmtm)
REVERT: C  304 ILE cc_start: 0.7882 (tt) cc_final: 0.7590 (mt)
REVERT: C  315 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7438 (ttm110)
REVERT: C  419 MET cc_start: 0.8824 (mmm) cc_final: 0.8562 (tpp)
REVERT: C  444 ASP cc_start: 0.7949 (t0) cc_final: 0.7683 (t70)
  outliers start: 28
  outliers final: 11
  residues processed: 176
  average time/residue: 1.1573
  time to fit residues: 218.7970
Evaluate side-chains
  168 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 153
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  235 ILE
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  445 ARG
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  269 CYS
Chi-restraints excluded: chain C residue  309 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0870
   chunk 86 optimal weight:    1.9990
   chunk 75 optimal weight:    0.2980
   chunk 23 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.4060 r_free = 0.4060 target = 0.190782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.159854 restraints weight = 2278.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 0.50
r_work: 0.3552 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.3427 rms_B_bonded: 2.29 restraints_weight: 0.2500
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9417  Z= 0.203
  Angle     :  0.514   5.844  12783  Z= 0.261
  Chirality :  0.039   0.145   1626
  Planarity :  0.004   0.034   1557
  Dihedral  :  3.802  33.078   1287
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 24.04 %
    Favored  : 73.29 %
  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:  1.72 (0.23), residues: 1200
  helix:  1.75 (0.16), residues: 924
  sheet: -0.24 (0.64), residues: 48
  loop : -1.03 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 256 
 HIS   0.002   0.001   HIS C 296 
 PHE   0.014   0.002   PHE B 240 
 TYR   0.011   0.001   TYR B 162 
 ARG   0.007   0.000   ARG A 353 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 174
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7737 (ttp80)
REVERT: A   75 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8141 (mmt)
REVERT: A   99 PHE cc_start: 0.8049 (t80) cc_final: 0.7638 (t80)
REVERT: A  117 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7669 (mttp)
REVERT: A  167 GLU cc_start: 0.7374 (pp20) cc_final: 0.6941 (pp20)
REVERT: A  272 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6917 (mp0)
REVERT: A  303 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7614 (tp)
REVERT: A  315 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7387 (ttm110)
REVERT: A  342 ARG cc_start: 0.7449 (ttm110) cc_final: 0.7214 (ttm110)
REVERT: A  444 ASP cc_start: 0.7865 (t0) cc_final: 0.7607 (t70)
REVERT: B   48 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7741 (mp0)
REVERT: B   68 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7466 (tp)
REVERT: B   99 PHE cc_start: 0.8026 (t80) cc_final: 0.7797 (t80)
REVERT: B  167 GLU cc_start: 0.7797 (pp20) cc_final: 0.7493 (pp20)
REVERT: B  258 MET cc_start: 0.8373 (tpp) cc_final: 0.8121 (tpt)
REVERT: B  277 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6425 (pm20)
REVERT: B  315 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7340 (ttm170)
REVERT: B  353 ARG cc_start: 0.7851 (mtm180) cc_final: 0.7603 (mpp-170)
REVERT: C   68 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7279 (tp)
REVERT: C  117 LYS cc_start: 0.8315 (mtmm) cc_final: 0.6667 (tmtt)
REVERT: C  205 MET cc_start: 0.8172 (ptt) cc_final: 0.7879 (ptm)
REVERT: C  228 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7557 (mmtm)
REVERT: C  277 GLU cc_start: 0.6489 (tm-30) cc_final: 0.6283 (pm20)
REVERT: C  304 ILE cc_start: 0.7898 (tt) cc_final: 0.7613 (mt)
REVERT: C  315 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7435 (ttm110)
REVERT: C  419 MET cc_start: 0.8860 (mmm) cc_final: 0.8585 (tpp)
REVERT: C  444 ASP cc_start: 0.7925 (t0) cc_final: 0.7685 (t70)
  outliers start: 27
  outliers final: 12
  residues processed: 190
  average time/residue: 1.2822
  time to fit residues: 261.0382
Evaluate side-chains
  173 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  235 ILE
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   66 ILE
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  269 CYS
Chi-restraints excluded: chain C residue  309 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 86 optimal weight:    0.1980
   chunk 72 optimal weight:    0.0980
   chunk 57 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0980
   chunk 113 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.3780

-------------------------------------------------------------------------------
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 = 0.4096 r_free = 0.4096 target = 0.194214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.163369 restraints weight = 2354.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 0.52
r_work: 0.3460 rms_B_bonded: 1.49 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 2.35 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9417  Z= 0.173
  Angle     :  0.509   7.097  12783  Z= 0.259
  Chirality :  0.038   0.141   1626
  Planarity :  0.004   0.033   1557
  Dihedral  :  3.708  32.027   1287
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 25.62 %
    Favored  : 72.60 %
  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:  1.83 (0.23), residues: 1200
  helix:  1.83 (0.16), residues: 927
  sheet: -0.30 (0.64), residues: 48
  loop : -0.97 (0.41), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 256 
 HIS   0.001   0.000   HIS B 296 
 PHE   0.011   0.001   PHE C 240 
 TYR   0.011   0.001   TYR B 162 
 ARG   0.007   0.000   ARG A 353 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 167
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7673 (ttp80)
REVERT: A   99 PHE cc_start: 0.7967 (t80) cc_final: 0.7572 (t80)
REVERT: A  117 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7629 (mttp)
REVERT: A  167 GLU cc_start: 0.7356 (pp20) cc_final: 0.6941 (pp20)
REVERT: A  272 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6953 (mp0)
REVERT: A  303 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7610 (tp)
REVERT: A  315 ARG cc_start: 0.7861 (ttm-80) cc_final: 0.7356 (ttm110)
REVERT: A  342 ARG cc_start: 0.7435 (ttm110) cc_final: 0.7220 (ttm110)
REVERT: A  444 ASP cc_start: 0.7798 (t0) cc_final: 0.7510 (t70)
REVERT: B   68 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7476 (tp)
REVERT: B   99 PHE cc_start: 0.7983 (t80) cc_final: 0.7722 (t80)
REVERT: B  140 ASP cc_start: 0.7953 (m-30) cc_final: 0.7639 (m-30)
REVERT: B  258 MET cc_start: 0.8378 (tpp) cc_final: 0.8098 (tpt)
REVERT: B  277 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6414 (pm20)
REVERT: B  315 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7324 (ttm170)
REVERT: B  353 ARG cc_start: 0.7823 (mtm180) cc_final: 0.7610 (mpp-170)
REVERT: B  419 MET cc_start: 0.8648 (tpt) cc_final: 0.8255 (mmt)
REVERT: B  440 ASP cc_start: 0.7726 (t70) cc_final: 0.7377 (t70)
REVERT: C   22 LEU cc_start: 0.8246 (mp) cc_final: 0.7867 (mt)
REVERT: C   68 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7343 (tp)
REVERT: C  205 MET cc_start: 0.8190 (ptt) cc_final: 0.7901 (ptm)
REVERT: C  228 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7574 (mmtm)
REVERT: C  304 ILE cc_start: 0.7894 (tt) cc_final: 0.7597 (mt)
REVERT: C  419 MET cc_start: 0.8814 (mmm) cc_final: 0.8549 (tpp)
REVERT: C  444 ASP cc_start: 0.7925 (t0) cc_final: 0.7669 (t70)
  outliers start: 18
  outliers final: 12
  residues processed: 178
  average time/residue: 1.1457
  time to fit residues: 219.0859
Evaluate side-chains
  172 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 157
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  269 CYS
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  235 ILE
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  269 CYS
Chi-restraints excluded: chain C residue  309 VAL
Chi-restraints excluded: chain C residue  396 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 61 optimal weight:    0.0170
   chunk 13 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 115 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.192416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.160378 restraints weight = 2433.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 0.54
r_work: 0.3535 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.3404 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9417  Z= 0.212
  Angle     :  0.541   8.608  12783  Z= 0.274
  Chirality :  0.039   0.144   1626
  Planarity :  0.004   0.034   1557
  Dihedral  :  3.812  32.071   1287
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 25.32 %
    Favored  : 72.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.23), residues: 1200
  helix:  1.78 (0.16), residues: 921
  sheet: -0.26 (0.65), residues: 48
  loop : -1.12 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 256 
 HIS   0.002   0.001   HIS B 296 
 PHE   0.015   0.002   PHE B 240 
 TYR   0.010   0.001   TYR B 162 
 ARG   0.007   0.000   ARG A 353 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6824.12 seconds
wall clock time: 120 minutes 58.51 seconds (7258.51 seconds total)