Starting phenix.real_space_refine
on Fri Feb 14 05:18:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8thi_41265/02_2025/8thi_41265.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8thi_41265/02_2025/8thi_41265.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8thi_41265/02_2025/8thi_41265.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8thi_41265/02_2025/8thi_41265.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8thi_41265/02_2025/8thi_41265.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8thi_41265/02_2025/8thi_41265.cif"
  }
  resolution = 3.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      66      5.16       5
     Na      2      4.78       5
     C    6392      2.51       5
     N    1464      2.21       5
     O    1593      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9519
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 613, 4739
          Classifications: {'peptide': 613}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 586}
    Chain: "B"
      Number of atoms: 4719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 611, 4719
          Classifications: {'peptide': 611}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 584}
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {' NA': 1, 'PGT': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 14
    Chain: "B"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {' NA': 1, 'PGT': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 29
  Time building chain proxies: 7.67, per 1000 atoms: 0.81
  Number of scatterers: 9519
  At special positions: 0
  Unit cell: (73.04, 88.312, 139.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      66     16.00
     P       2     15.00
     Na      2     11.00
     O    1593      8.00
     N    1464      7.00
     C    6392      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: 2.86
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2264

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 0 sheets defined
      87.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
    Processing helix  chain 'A' and resid 39 through 63
      removed outlier: 3.757A  pdb=" N   TYR A  50 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 75
      removed outlier: 3.735A  pdb=" N   MET A  75 " --> pdb=" O   THR A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 108
      removed outlier: 4.445A  pdb=" N   PHE A  82 " --> pdb=" O   LYS A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 126
    Processing helix  chain 'A' and resid 126 through 149
      removed outlier: 3.881A  pdb=" N   VAL A 130 " --> pdb=" O   ALA A 126 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU A 134 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   THR A 144 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LEU A 145 " --> pdb=" O   GLN A 141 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR A 149 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 173
      removed outlier: 3.787A  pdb=" N   PHE A 159 " --> pdb=" O   PRO A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 180
      removed outlier: 3.733A  pdb=" N   PHE A 177 " --> pdb=" O   PRO A 174 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LYS A 178 " --> pdb=" O   ASP A 175 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   VAL A 179 " --> pdb=" O   TRP A 176 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU A 180 " --> pdb=" O   PHE A 177 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 174 through 180'
    Processing helix  chain 'A' and resid 181 through 185
    Processing helix  chain 'A' and resid 191 through 205
    Processing helix  chain 'A' and resid 209 through 226
      removed outlier: 4.222A  pdb=" N   PHE A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 234
      removed outlier: 3.763A  pdb=" N   ALA A 233 " --> pdb=" O   VAL A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 242
      removed outlier: 4.471A  pdb=" N   VAL A 238 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   LEU A 241 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASP A 242 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 246
      No H-bonds generated for 'chain 'A' and resid 244 through 246'
    Processing helix  chain 'A' and resid 247 through 260
      removed outlier: 4.134A  pdb=" N   PHE A 251 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 277
    Processing helix  chain 'A' and resid 281 through 296
      removed outlier: 3.668A  pdb=" N   GLY A 296 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 320
      removed outlier: 3.592A  pdb=" N   LEU A 308 " --> pdb=" O   ASP A 304 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   GLN A 310 " --> pdb=" O   GLY A 306 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   LEU A 311 " --> pdb=" O   GLY A 307 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LYS A 314 " --> pdb=" O   GLN A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 333
    Processing helix  chain 'A' and resid 335 through 340
      removed outlier: 3.897A  pdb=" N   LEU A 339 " --> pdb=" O   ILE A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 354
    Processing helix  chain 'A' and resid 356 through 387
      removed outlier: 4.435A  pdb=" N   ILE A 366 " --> pdb=" O   ILE A 362 " (cutoff:3.500A)
      Proline residue:  A 367  - end of helix
    Processing helix  chain 'A' and resid 395 through 422
      removed outlier: 5.324A  pdb=" N   TRP A 408 " --> pdb=" O   LYS A 404 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   ALA A 409 " --> pdb=" O   GLN A 405 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   THR A 412 " --> pdb=" O   TRP A 408 " (cutoff:3.500A)
      Proline residue:  A 413  - end of helix
    Processing helix  chain 'A' and resid 426 through 445
    Processing helix  chain 'A' and resid 450 through 485
      removed outlier: 3.969A  pdb=" N   VAL A 467 " --> pdb=" O   ALA A 463 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   VAL A 468 " --> pdb=" O   ILE A 464 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   MET A 471 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ASP A 480 " --> pdb=" O   THR A 476 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   MET A 481 " --> pdb=" O   PHE A 477 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   GLU A 485 " --> pdb=" O   MET A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 495
    Processing helix  chain 'A' and resid 501 through 517
      removed outlier: 3.839A  pdb=" N   VAL A 505 " --> pdb=" O   SER A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 540
      removed outlier: 3.786A  pdb=" N   PHE A 527 " --> pdb=" O   LEU A 523 " (cutoff:3.500A)
      Proline residue:  A 531  - end of helix
      Proline residue:  A 535  - end of helix
    Processing helix  chain 'A' and resid 543 through 558
      removed outlier: 3.583A  pdb=" N   GLY A 558 " --> pdb=" O   ASN A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 561
      No H-bonds generated for 'chain 'A' and resid 559 through 561'
    Processing helix  chain 'A' and resid 565 through 576
    Processing helix  chain 'A' and resid 578 through 587
    Processing helix  chain 'A' and resid 589 through 603
      removed outlier: 4.493A  pdb=" N   VAL A 593 " --> pdb=" O   PHE A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 615
      removed outlier: 4.599A  pdb=" N   VAL A 610 " --> pdb=" O   ILE A 606 " (cutoff:3.500A)
      Proline residue:  A 611  - end of helix
    Processing helix  chain 'B' and resid 6 through 32
    Processing helix  chain 'B' and resid 39 through 63
      removed outlier: 3.799A  pdb=" N   TYR B  50 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 75
      removed outlier: 4.048A  pdb=" N   MET B  75 " --> pdb=" O   THR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 109
      removed outlier: 3.692A  pdb=" N   PHE B  82 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 117
      removed outlier: 3.975A  pdb=" N   GLY B 117 " --> pdb=" O   ASP B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 126
    Processing helix  chain 'B' and resid 126 through 149
      removed outlier: 3.809A  pdb=" N   VAL B 130 " --> pdb=" O   ALA B 126 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL B 131 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU B 134 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR B 144 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   LEU B 145 " --> pdb=" O   GLN B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 173
      removed outlier: 3.767A  pdb=" N   PHE B 159 " --> pdb=" O   PRO B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 180
      removed outlier: 3.725A  pdb=" N   VAL B 179 " --> pdb=" O   TRP B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 185
    Processing helix  chain 'B' and resid 191 through 207
      removed outlier: 3.596A  pdb=" N   GLY B 207 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 226
      removed outlier: 4.251A  pdb=" N   PHE B 215 " --> pdb=" O   GLY B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 234
    Processing helix  chain 'B' and resid 234 through 240
      removed outlier: 4.252A  pdb=" N   VAL B 238 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 246
      No H-bonds generated for 'chain 'B' and resid 244 through 246'
    Processing helix  chain 'B' and resid 247 through 260
      removed outlier: 4.074A  pdb=" N   PHE B 251 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 277
    Processing helix  chain 'B' and resid 281 through 296
    Processing helix  chain 'B' and resid 300 through 308
      removed outlier: 3.820A  pdb=" N   ASP B 304 " --> pdb=" O   SER B 300 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU B 308 " --> pdb=" O   ASP B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 320
    Processing helix  chain 'B' and resid 322 through 333
    Processing helix  chain 'B' and resid 335 through 340
      removed outlier: 3.986A  pdb=" N   LEU B 339 " --> pdb=" O   ILE B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 354
    Processing helix  chain 'B' and resid 356 through 387
      removed outlier: 4.360A  pdb=" N   ILE B 366 " --> pdb=" O   ILE B 362 " (cutoff:3.500A)
      Proline residue:  B 367  - end of helix
    Processing helix  chain 'B' and resid 395 through 423
      removed outlier: 5.638A  pdb=" N   TRP B 408 " --> pdb=" O   LYS B 404 " (cutoff:3.500A)
      removed outlier: 5.484A  pdb=" N   ALA B 409 " --> pdb=" O   GLN B 405 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   THR B 412 " --> pdb=" O   TRP B 408 " (cutoff:3.500A)
      Proline residue:  B 413  - end of helix
      removed outlier: 3.745A  pdb=" N   GLY B 423 " --> pdb=" O   GLY B 419 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 445
    Processing helix  chain 'B' and resid 450 through 485
      removed outlier: 4.054A  pdb=" N   VAL B 467 " --> pdb=" O   ALA B 463 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   VAL B 468 " --> pdb=" O   ILE B 464 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ASP B 480 " --> pdb=" O   THR B 476 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   MET B 481 " --> pdb=" O   PHE B 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 486 through 495
      removed outlier: 3.533A  pdb=" N   ARG B 490 " --> pdb=" O   GLN B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 500
      removed outlier: 3.768A  pdb=" N   ASP B 500 " --> pdb=" O   ALA B 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 517
      removed outlier: 3.630A  pdb=" N   VAL B 505 " --> pdb=" O   SER B 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 521 through 540
      Proline residue:  B 531  - end of helix
      Proline residue:  B 535  - end of helix
    Processing helix  chain 'B' and resid 543 through 558
      removed outlier: 3.658A  pdb=" N   GLY B 558 " --> pdb=" O   ASN B 554 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 561
      No H-bonds generated for 'chain 'B' and resid 559 through 561'
    Processing helix  chain 'B' and resid 565 through 576
      removed outlier: 3.520A  pdb=" N   PHE B 569 " --> pdb=" O   GLY B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 578 through 587
    Processing helix  chain 'B' and resid 589 through 603
      removed outlier: 4.395A  pdb=" N   VAL B 593 " --> pdb=" O   PHE B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 603 through 615
      removed outlier: 4.450A  pdb=" N   ILE B 607 " --> pdb=" O   PHE B 603 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   VAL B 610 " --> pdb=" O   ILE B 606 " (cutoff:3.500A)
      Proline residue:  B 611  - end of helix

    699 hydrogen bonds defined for protein.
    2061 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.84

  Time building geometry restraints manager: 3.24 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1427
        1.32 -     1.44: 2580
        1.44 -     1.56: 5611
        1.56 -     1.69: 4
        1.69 -     1.81: 122
  Bond restraints: 9744
  Sorted by residual:
  bond pdb=" N   ILE A   4 "
       pdb=" CA  ILE A   4 "
    ideal  model  delta    sigma   weight residual
    1.459  1.504 -0.045 1.25e-02 6.40e+03 1.32e+01
  bond pdb=" N   THR A 280 "
       pdb=" CA  THR A 280 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.29e-02 6.01e+03 7.19e+00
  bond pdb=" N   ASN A   5 "
       pdb=" CA  ASN A   5 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.36e-02 5.41e+03 6.43e+00
  bond pdb=" N   LYS A 178 "
       pdb=" CA  LYS A 178 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.033 1.31e-02 5.83e+03 6.36e+00
  bond pdb=" N   VAL B 498 "
       pdb=" CA  VAL B 498 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.33e-02 5.65e+03 6.35e+00
  ... (remaining 9739 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 12758
        1.14 -     2.28: 366
        2.28 -     3.42: 79
        3.42 -     4.56: 15
        4.56 -     5.70: 20
  Bond angle restraints: 13238
  Sorted by residual:
  angle pdb=" N   VAL A 498 "
        pdb=" CA  VAL A 498 "
        pdb=" C   VAL A 498 "
      ideal   model   delta    sigma   weight residual
     113.10  110.06    3.04 9.70e-01 1.06e+00 9.81e+00
  angle pdb=" C   GLY A 282 "
        pdb=" N   MET A 283 "
        pdb=" CA  MET A 283 "
      ideal   model   delta    sigma   weight residual
     120.31  115.67    4.64 1.52e+00 4.33e-01 9.33e+00
  angle pdb=" N   ASN A   5 "
        pdb=" CA  ASN A   5 "
        pdb=" C   ASN A   5 "
      ideal   model   delta    sigma   weight residual
     114.04  110.50    3.54 1.24e+00 6.50e-01 8.16e+00
  angle pdb=" CA  ASP B 500 "
        pdb=" C   ASP B 500 "
        pdb=" O   ASP B 500 "
      ideal   model   delta    sigma   weight residual
     121.07  117.93    3.14 1.10e+00 8.26e-01 8.14e+00
  angle pdb=" N   LYS A 178 "
        pdb=" CA  LYS A 178 "
        pdb=" C   LYS A 178 "
      ideal   model   delta    sigma   weight residual
     113.18  109.97    3.21 1.21e+00 6.83e-01 7.06e+00
  ... (remaining 13233 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.30: 5031
       16.30 -    32.61: 529
       32.61 -    48.91: 120
       48.91 -    65.21: 23
       65.21 -    81.51: 5
  Dihedral angle restraints: 5708
    sinusoidal: 2193
      harmonic: 3515
  Sorted by residual:
  dihedral pdb=" CB  MET B 556 "
           pdb=" CG  MET B 556 "
           pdb=" SD  MET B 556 "
           pdb=" CE  MET B 556 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  114.20  -54.20     3      1.50e+01 4.44e-03 9.26e+00
  dihedral pdb=" CB  LYS B 236 "
           pdb=" CG  LYS B 236 "
           pdb=" CD  LYS B 236 "
           pdb=" CE  LYS B 236 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -114.11   54.11     3      1.50e+01 4.44e-03 9.26e+00
  dihedral pdb=" CB  MET A 556 "
           pdb=" CG  MET A 556 "
           pdb=" SD  MET A 556 "
           pdb=" CE  MET A 556 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  114.10  -54.10     3      1.50e+01 4.44e-03 9.26e+00
  ... (remaining 5705 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1255
       0.046 -    0.091: 299
       0.091 -    0.137: 45
       0.137 -    0.183: 1
       0.183 -    0.229: 3
  Chirality restraints: 1603
  Sorted by residual:
  chirality pdb=" CB  ILE A   4 "
            pdb=" CA  ILE A   4 "
            pdb=" CG1 ILE A   4 "
            pdb=" CG2 ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CB  VAL B 498 "
            pdb=" CA  VAL B 498 "
            pdb=" CG1 VAL B 498 "
            pdb=" CG2 VAL B 498 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  VAL B 498 "
            pdb=" N   VAL B 498 "
            pdb=" C   VAL B 498 "
            pdb=" CB  VAL B 498 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.21e-01
  ... (remaining 1600 not shown)

  Planarity restraints: 1597
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 281 "    0.011 2.00e-02 2.50e+03   2.16e-02 4.67e+00
        pdb=" C   GLY A 281 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   GLY A 281 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLY A 282 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 498 "   -0.008 2.00e-02 2.50e+03   1.62e-02 2.63e+00
        pdb=" C   VAL B 498 "    0.028 2.00e-02 2.50e+03
        pdb=" O   VAL B 498 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ALA B 499 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 426 "    0.022 5.00e-02 4.00e+02   3.26e-02 1.70e+00
        pdb=" N   PRO A 427 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 427 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 427 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1594 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1184
        2.75 -     3.29: 9613
        3.29 -     3.82: 15789
        3.82 -     4.36: 17014
        4.36 -     4.90: 31284
  Nonbonded interactions: 74884
  Sorted by model distance:
  nonbonded pdb=" O   SER A 298 "
            pdb="NA    NA A 702 "
     model   vdw
     2.209 2.470
  nonbonded pdb=" O   VAL B 179 "
            pdb=" OH  TYR B 185 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   GLY A 277 "
            pdb=" OG1 THR A 391 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   THR B 450 "
            pdb=" OG  SER B 453 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   GLY A 337 "
            pdb="NA    NA A 702 "
     model   vdw
     2.303 2.470
  ... (remaining 74879 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 5 through 615 or (resid 701 and (name C1 or name C11 or na \ 
me C12 or name C2 or name C3 or name C31 or name C32 or name C33 or name C4 or n \ 
ame C5 or name C6 or name O11 or name O1P or name O2 or name O2P or name O3 or n \ 
ame O31 or name O3P or name O4P or name O5 or name O6 or name P )) or resid 702) \ 
)
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.730
  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:             0.020
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     26.230
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
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   0.045   9744  Z= 0.196
  Angle     :  0.510   5.699  13238  Z= 0.290
  Chirality :  0.038   0.229   1603
  Planarity :  0.003   0.033   1597
  Dihedral  : 13.987  81.514   3444
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.05 %
    Favored  : 96.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  2.97 (0.25), residues: 1220
  helix:  2.44 (0.17), residues: 954
  sheet:  None (None), residues: 0
  loop :  0.27 (0.41), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 200 
 HIS   0.002   0.001   HIS B 100 
 PHE   0.014   0.001   PHE B  98 
 TYR   0.010   0.001   TYR A   3 
 ARG   0.002   0.000   ARG A 226 

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 183
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 MET cc_start: 0.7850 (mtp) cc_final: 0.7553 (mtm)
REVERT: A  178 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7069 (mmtt)
REVERT: A  198 LEU cc_start: 0.8513 (tp) cc_final: 0.8178 (mp)
REVERT: A  264 ILE cc_start: 0.8538 (mt) cc_final: 0.8323 (tp)
REVERT: A  508 MET cc_start: 0.8623 (mmt) cc_final: 0.8415 (mmm)
REVERT: A  566 MET cc_start: 0.8181 (mmm) cc_final: 0.7977 (mmt)
REVERT: B   10 TRP cc_start: 0.8262 (m100) cc_final: 0.7987 (m100)
REVERT: B  564 MET cc_start: 0.8459 (tpp) cc_final: 0.7890 (tpp)
  outliers start: 3
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1675
  time to fit residues: 46.8742
Evaluate side-chains
  114 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 95 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 71 optimal weight:    8.9990
   chunk 110 optimal weight:    0.0470
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 228 ASN
A 486 GLN
B 143 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.098147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.076000 restraints weight = 23661.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 3.08
r_work: 0.3100 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9744  Z= 0.183
  Angle     :  0.547  10.715  13238  Z= 0.273
  Chirality :  0.039   0.153   1603
  Planarity :  0.004   0.033   1597
  Dihedral  :  5.907  64.822   1340
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  8.64 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  3.03 (0.25), residues: 1220
  helix:  2.48 (0.17), residues: 958
  sheet:  None (None), residues: 0
  loop :  0.27 (0.42), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  10 
 HIS   0.003   0.001   HIS A 285 
 PHE   0.018   0.001   PHE A 158 
 TYR   0.013   0.001   TYR A 349 
 ARG   0.003   0.000   ARG A  30 

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 1.027 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.8787 (m100) cc_final: 0.8358 (m100)
REVERT: A  264 ILE cc_start: 0.8659 (mt) cc_final: 0.8444 (tp)
REVERT: A  508 MET cc_start: 0.8688 (mmt) cc_final: 0.8421 (mmm)
REVERT: B   10 TRP cc_start: 0.8658 (m100) cc_final: 0.8414 (m100)
REVERT: B  204 MET cc_start: 0.8472 (tpp) cc_final: 0.8123 (tpt)
REVERT: B  224 MET cc_start: 0.7675 (mtm) cc_final: 0.7388 (mtm)
REVERT: B  316 MET cc_start: 0.6946 (mtp) cc_final: 0.6711 (mtp)
REVERT: B  376 MET cc_start: 0.6797 (mmt) cc_final: 0.6534 (mmt)
REVERT: B  378 MET cc_start: 0.8666 (tpp) cc_final: 0.8268 (tpp)
REVERT: B  564 MET cc_start: 0.8469 (tpp) cc_final: 0.7938 (tpp)
REVERT: B  566 MET cc_start: 0.8304 (mmm) cc_final: 0.8101 (mmm)
  outliers start: 16
  outliers final: 6
  residues processed: 129
  average time/residue: 0.1648
  time to fit residues: 32.9390
Evaluate side-chains
  115 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  333 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 53 optimal weight:    0.3980
   chunk 51 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 121 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 92 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 72 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 260 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.097248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.074850 restraints weight = 23815.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 3.13
r_work: 0.3067 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9744  Z= 0.179
  Angle     :  0.538   8.477  13238  Z= 0.269
  Chirality :  0.039   0.161   1603
  Planarity :  0.004   0.034   1597
  Dihedral  :  5.906  65.722   1336
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.92 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  2.96 (0.25), residues: 1220
  helix:  2.38 (0.17), residues: 967
  sheet:  None (None), residues: 0
  loop :  0.36 (0.42), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 408 
 HIS   0.003   0.001   HIS B 285 
 PHE   0.019   0.001   PHE B  20 
 TYR   0.014   0.001   TYR A 349 
 ARG   0.004   0.000   ARG B 396 

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 1.117 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.8805 (m100) cc_final: 0.8378 (m100)
REVERT: A  508 MET cc_start: 0.8715 (mmt) cc_final: 0.8442 (mmm)
REVERT: B  204 MET cc_start: 0.8497 (tpp) cc_final: 0.8254 (tpt)
REVERT: B  224 MET cc_start: 0.7676 (mtm) cc_final: 0.7391 (mtm)
REVERT: B  378 MET cc_start: 0.8789 (tpp) cc_final: 0.8413 (tpp)
REVERT: B  564 MET cc_start: 0.8511 (tpp) cc_final: 0.8005 (tpp)
  outliers start: 21
  outliers final: 14
  residues processed: 127
  average time/residue: 0.1619
  time to fit residues: 32.3580
Evaluate side-chains
  117 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  400 CYS
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  577 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 100 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0270
   chunk 62 optimal weight:   10.0000
   chunk 19 optimal weight:    0.7980
   chunk 105 optimal weight:    9.9990
   chunk 114 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 80 optimal weight:    0.7980
   chunk 120 optimal weight:    2.9990
   overall best weight:    0.6238

-------------------------------------------------------------------------------
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 = 0.3623 r_free = 0.3623 target = 0.097705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.075047 restraints weight = 23892.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 3.16
r_work: 0.3064 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   9744  Z= 0.162
  Angle     :  0.515   6.794  13238  Z= 0.257
  Chirality :  0.038   0.149   1603
  Planarity :  0.004   0.037   1597
  Dihedral  :  5.681  66.538   1336
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.30 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.92 (0.25), residues: 1220
  helix:  2.35 (0.17), residues: 967
  sheet:  None (None), residues: 0
  loop :  0.34 (0.42), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 408 
 HIS   0.002   0.001   HIS A 100 
 PHE   0.023   0.001   PHE A 251 
 TYR   0.008   0.001   TYR B 221 
 ARG   0.001   0.000   ARG B  80 

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 1.011 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.8809 (m100) cc_final: 0.8444 (m100)
REVERT: A  164 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8314 (m)
REVERT: A  508 MET cc_start: 0.8723 (mmt) cc_final: 0.8450 (mmm)
REVERT: B   10 TRP cc_start: 0.8680 (m100) cc_final: 0.7901 (m100)
REVERT: B  204 MET cc_start: 0.8581 (tpp) cc_final: 0.8339 (tpt)
REVERT: B  378 MET cc_start: 0.8806 (tpp) cc_final: 0.8424 (tpp)
REVERT: B  471 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7966 (mtm)
REVERT: B  564 MET cc_start: 0.8526 (tpp) cc_final: 0.8215 (tpp)
  outliers start: 17
  outliers final: 13
  residues processed: 114
  average time/residue: 0.1637
  time to fit residues: 29.3296
Evaluate side-chains
  113 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  400 CYS
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  471 MET
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  577 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 117 optimal weight:    0.0980
   chunk 24 optimal weight:    0.2980
   chunk 90 optimal weight:    0.0060
   chunk 25 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 60 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.3396

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

Flipped N/Q/H residues before XYZ refinement:
A 612 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.098423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.075952 restraints weight = 23804.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 3.11
r_work: 0.3090 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9744  Z= 0.142
  Angle     :  0.513  11.076  13238  Z= 0.251
  Chirality :  0.038   0.129   1603
  Planarity :  0.004   0.042   1597
  Dihedral  :  5.474  66.195   1336
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 12.57 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  2.94 (0.25), residues: 1220
  helix:  2.36 (0.17), residues: 965
  sheet:  None (None), residues: 0
  loop :  0.38 (0.42), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 408 
 HIS   0.002   0.001   HIS A 100 
 PHE   0.021   0.001   PHE A  98 
 TYR   0.011   0.001   TYR B 221 
 ARG   0.001   0.000   ARG B  80 

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 1.191 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.8795 (m100) cc_final: 0.8455 (m100)
REVERT: A  508 MET cc_start: 0.8717 (mmt) cc_final: 0.8435 (mmm)
REVERT: B   10 TRP cc_start: 0.8641 (m100) cc_final: 0.7826 (m100)
REVERT: B  204 MET cc_start: 0.8599 (tpp) cc_final: 0.8383 (tpt)
REVERT: B  291 SER cc_start: 0.8543 (t) cc_final: 0.8338 (m)
REVERT: B  378 MET cc_start: 0.8811 (tpp) cc_final: 0.8424 (tpp)
REVERT: B  471 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7943 (mtm)
REVERT: B  564 MET cc_start: 0.8517 (tpp) cc_final: 0.8232 (tpp)
  outliers start: 19
  outliers final: 10
  residues processed: 112
  average time/residue: 0.1675
  time to fit residues: 29.5688
Evaluate side-chains
  109 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  471 MET
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  577 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0010
   chunk 90 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 65 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0370
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.5064

-------------------------------------------------------------------------------
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 = 0.3630 r_free = 0.3630 target = 0.098097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.075556 restraints weight = 23880.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 3.13
r_work: 0.3081 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9744  Z= 0.147
  Angle     :  0.514   9.991  13238  Z= 0.253
  Chirality :  0.038   0.126   1603
  Planarity :  0.004   0.044   1597
  Dihedral  :  5.248  63.413   1336
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.06 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  2.98 (0.25), residues: 1220
  helix:  2.38 (0.17), residues: 966
  sheet:  None (None), residues: 0
  loop :  0.42 (0.42), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 408 
 HIS   0.003   0.001   HIS A 100 
 PHE   0.020   0.001   PHE B 167 
 TYR   0.008   0.001   TYR B 221 
 ARG   0.003   0.000   ARG B 226 

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.8773 (m100) cc_final: 0.8454 (m100)
REVERT: A  508 MET cc_start: 0.8751 (mmt) cc_final: 0.8467 (mmm)
REVERT: B   10 TRP cc_start: 0.8652 (m100) cc_final: 0.7914 (m100)
REVERT: B   98 PHE cc_start: 0.9169 (t80) cc_final: 0.8629 (t80)
REVERT: B  260 ASN cc_start: 0.8723 (p0) cc_final: 0.8242 (t0)
REVERT: B  291 SER cc_start: 0.8556 (t) cc_final: 0.8350 (m)
REVERT: B  378 MET cc_start: 0.8835 (tpp) cc_final: 0.8468 (tpp)
REVERT: B  471 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.7977 (mtm)
REVERT: B  564 MET cc_start: 0.8510 (tpp) cc_final: 0.8233 (tpp)
  outliers start: 16
  outliers final: 11
  residues processed: 111
  average time/residue: 0.1580
  time to fit residues: 27.7413
Evaluate side-chains
  109 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  400 CYS
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  471 MET
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  577 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 88 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 121 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 111 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 278 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.096906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.074190 restraints weight = 24130.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 3.15
r_work: 0.3051 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9744  Z= 0.176
  Angle     :  0.529  10.023  13238  Z= 0.259
  Chirality :  0.038   0.148   1603
  Planarity :  0.004   0.047   1597
  Dihedral  :  5.190  61.839   1336
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 13.46 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.96 (0.25), residues: 1220
  helix:  2.40 (0.17), residues: 959
  sheet:  None (None), residues: 0
  loop :  0.36 (0.41), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 408 
 HIS   0.003   0.001   HIS A 100 
 PHE   0.020   0.001   PHE B 167 
 TYR   0.007   0.001   TYR B 380 
 ARG   0.001   0.000   ARG A 104 

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 1.055 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.8797 (m100) cc_final: 0.8429 (m100)
REVERT: A  343 SER cc_start: 0.8300 (t) cc_final: 0.7886 (p)
REVERT: A  508 MET cc_start: 0.8766 (mmt) cc_final: 0.8492 (mmm)
REVERT: B   10 TRP cc_start: 0.8672 (m100) cc_final: 0.7930 (m100)
REVERT: B   53 MET cc_start: 0.9458 (mmm) cc_final: 0.9224 (mmm)
REVERT: B   98 PHE cc_start: 0.9194 (t80) cc_final: 0.8651 (t80)
REVERT: B  260 ASN cc_start: 0.8696 (p0) cc_final: 0.8242 (t0)
REVERT: B  291 SER cc_start: 0.8587 (t) cc_final: 0.8381 (m)
REVERT: B  378 MET cc_start: 0.8861 (tpp) cc_final: 0.8458 (tpp)
REVERT: B  467 VAL cc_start: 0.7505 (OUTLIER) cc_final: 0.7189 (p)
REVERT: B  471 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8016 (mtm)
REVERT: B  564 MET cc_start: 0.8513 (tpp) cc_final: 0.8237 (tpp)
  outliers start: 17
  outliers final: 11
  residues processed: 112
  average time/residue: 0.1634
  time to fit residues: 28.5632
Evaluate side-chains
  113 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 THR
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  471 MET
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  577 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 105 optimal weight:    5.9990
   chunk 79 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3577 r_free = 0.3577 target = 0.094885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.071929 restraints weight = 24276.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 3.11
r_work: 0.3007 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.3518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9744  Z= 0.233
  Angle     :  0.568  10.089  13238  Z= 0.280
  Chirality :  0.039   0.144   1603
  Planarity :  0.004   0.042   1597
  Dihedral  :  5.309  61.080   1336
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 13.85 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  2.91 (0.25), residues: 1220
  helix:  2.36 (0.17), residues: 958
  sheet:  None (None), residues: 0
  loop :  0.35 (0.41), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 408 
 HIS   0.003   0.001   HIS A 100 
 PHE   0.023   0.001   PHE B 167 
 TYR   0.010   0.001   TYR B 380 
 ARG   0.003   0.000   ARG A 381 

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 1.000 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.8834 (m100) cc_final: 0.8390 (m100)
REVERT: A  316 MET cc_start: 0.8041 (mtp) cc_final: 0.7835 (mtp)
REVERT: A  508 MET cc_start: 0.8813 (mmt) cc_final: 0.8533 (mmm)
REVERT: B   10 TRP cc_start: 0.8690 (m100) cc_final: 0.7970 (m100)
REVERT: B   98 PHE cc_start: 0.9188 (t80) cc_final: 0.8617 (t80)
REVERT: B  224 MET cc_start: 0.7980 (ptp) cc_final: 0.7707 (ptp)
REVERT: B  260 ASN cc_start: 0.8717 (p0) cc_final: 0.8248 (t0)
REVERT: B  378 MET cc_start: 0.8900 (tpp) cc_final: 0.8538 (tpp)
REVERT: B  467 VAL cc_start: 0.7710 (OUTLIER) cc_final: 0.7315 (p)
REVERT: B  471 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8151 (mtm)
REVERT: B  564 MET cc_start: 0.8483 (tpp) cc_final: 0.8212 (tpp)
  outliers start: 19
  outliers final: 14
  residues processed: 111
  average time/residue: 0.1702
  time to fit residues: 29.5138
Evaluate side-chains
  114 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 THR
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  471 MET
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  577 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 83 optimal weight:    0.0770
   chunk 74 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0370
   chunk 102 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 112 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 70 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.4216

-------------------------------------------------------------------------------
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 = 0.3617 r_free = 0.3617 target = 0.097492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.075066 restraints weight = 23949.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 3.11
r_work: 0.3061 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   9744  Z= 0.155
  Angle     :  0.550   9.893  13238  Z= 0.266
  Chirality :  0.038   0.177   1603
  Planarity :  0.004   0.047   1597
  Dihedral  :  5.289  62.119   1336
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 14.93 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  2.95 (0.25), residues: 1220
  helix:  2.38 (0.17), residues: 956
  sheet:  None (None), residues: 0
  loop :  0.40 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 408 
 HIS   0.002   0.001   HIS A 100 
 PHE   0.026   0.001   PHE B 167 
 TYR   0.007   0.001   TYR B 380 
 ARG   0.002   0.000   ARG A 381 

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.892 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.8781 (m100) cc_final: 0.8419 (m100)
REVERT: A  508 MET cc_start: 0.8748 (mmt) cc_final: 0.8466 (mmm)
REVERT: B   10 TRP cc_start: 0.8669 (m100) cc_final: 0.7965 (m100)
REVERT: B   98 PHE cc_start: 0.9154 (t80) cc_final: 0.8552 (t80)
REVERT: B  224 MET cc_start: 0.7832 (ptp) cc_final: 0.7626 (ptp)
REVERT: B  260 ASN cc_start: 0.8637 (p0) cc_final: 0.8162 (t0)
REVERT: B  378 MET cc_start: 0.8835 (tpp) cc_final: 0.8455 (tpp)
REVERT: B  467 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7238 (p)
REVERT: B  471 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8050 (mtm)
REVERT: B  481 MET cc_start: 0.9284 (tmm) cc_final: 0.8849 (tmm)
REVERT: B  564 MET cc_start: 0.8466 (tpp) cc_final: 0.8151 (tpp)
  outliers start: 11
  outliers final: 7
  residues processed: 106
  average time/residue: 0.1680
  time to fit residues: 27.8267
Evaluate side-chains
  107 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  471 MET
Chi-restraints excluded: chain B residue  529 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 78 optimal weight:    0.0170
   chunk 52 optimal weight:    0.8980
   chunk 46 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
B  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.097136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.074530 restraints weight = 24535.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 3.18
r_work: 0.3054 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.3765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9744  Z= 0.162
  Angle     :  0.546  10.810  13238  Z= 0.264
  Chirality :  0.038   0.190   1603
  Planarity :  0.004   0.044   1597
  Dihedral  :  5.236  62.201   1336
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 15.23 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  2.97 (0.25), residues: 1220
  helix:  2.40 (0.17), residues: 956
  sheet:  None (None), residues: 0
  loop :  0.40 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 408 
 HIS   0.003   0.001   HIS A 100 
 PHE   0.025   0.001   PHE B 167 
 TYR   0.008   0.001   TYR A 321 
 ARG   0.002   0.000   ARG B 138 

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 1.070 
Fit side-chains
REVERT: A   10 TRP cc_start: 0.8767 (m100) cc_final: 0.8406 (m100)
REVERT: A  508 MET cc_start: 0.8745 (mmt) cc_final: 0.8472 (mmm)
REVERT: B   10 TRP cc_start: 0.8663 (m100) cc_final: 0.7984 (m100)
REVERT: B   98 PHE cc_start: 0.9142 (t80) cc_final: 0.8512 (t80)
REVERT: B  224 MET cc_start: 0.7883 (ptp) cc_final: 0.7650 (ptp)
REVERT: B  260 ASN cc_start: 0.8662 (p0) cc_final: 0.8200 (t0)
REVERT: B  378 MET cc_start: 0.8844 (tpp) cc_final: 0.8462 (tpp)
REVERT: B  467 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7278 (p)
REVERT: B  471 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8093 (mtm)
REVERT: B  481 MET cc_start: 0.9279 (tmm) cc_final: 0.8877 (tmm)
REVERT: B  564 MET cc_start: 0.8458 (tpp) cc_final: 0.8154 (tpp)
  outliers start: 12
  outliers final: 9
  residues processed: 106
  average time/residue: 0.1625
  time to fit residues: 27.2276
Evaluate side-chains
  109 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 THR
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  471 MET
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  577 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 115 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 114 optimal weight:    0.4980
   chunk 52 optimal weight:    0.4980
   chunk 43 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 119 optimal weight:    0.2980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3621 r_free = 0.3621 target = 0.097661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.075327 restraints weight = 24104.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 3.13
r_work: 0.3069 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.3853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9744  Z= 0.156
  Angle     :  0.545  10.968  13238  Z= 0.262
  Chirality :  0.038   0.194   1603
  Planarity :  0.004   0.041   1597
  Dihedral  :  5.215  62.893   1336
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.44 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  2.91 (0.25), residues: 1220
  helix:  2.33 (0.17), residues: 965
  sheet:  None (None), residues: 0
  loop :  0.43 (0.41), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 408 
 HIS   0.003   0.001   HIS A 100 
 PHE   0.026   0.001   PHE B 167 
 TYR   0.009   0.001   TYR A 321 
 ARG   0.001   0.000   ARG B 181 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4161.01 seconds
wall clock time: 74 minutes 57.45 seconds (4497.45 seconds total)