Starting phenix.real_space_refine
on Fri Aug 22 16:32:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hiw_34828/08_2025/8hiw_34828.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hiw_34828/08_2025/8hiw_34828.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hiw_34828/08_2025/8hiw_34828.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hiw_34828/08_2025/8hiw_34828.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hiw_34828/08_2025/8hiw_34828.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hiw_34828/08_2025/8hiw_34828.cif"
  }
  resolution = 3.34
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=  -0.001 sd=   0.096
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 13 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    3888      2.51       5
     N     958      2.21       5
     O    1069      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5945
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2966
          Classifications: {'peptide': 384}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 12, 'TRANS': 371}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 87
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 43
    Chain: "B"
      Number of atoms: 2966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2966
          Classifications: {'peptide': 384}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 12, 'TRANS': 371}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 87
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 43
    Chain: "B"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Unusual residues: {'CIT': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C1  CIT B 601 " occ=0.50
      ... (11 atoms not shown)
      pdb=" O7  CIT B 601 " occ=0.50
  Time building chain proxies: 1.29, per 1000 atoms: 0.22
  Number of scatterers: 5945
  At special positions: 0
  Unit cell: (80.565, 78.4166, 108.494, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    1069      8.00
     N     958      7.00
     C    3888      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: 0.40
  Conformation dependent library (CDL) restraints added in 299.7 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 0 sheets defined
      80.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 67 through 84
      removed outlier: 3.533A  pdb=" N   ASP A  72 " --> pdb=" O   ASP A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 109
    Processing helix  chain 'A' and resid 117 through 128
      removed outlier: 3.744A  pdb=" N   ALA A 121 " --> pdb=" O   TYR A 117 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE A 122 " --> pdb=" O   SER A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 163
    Processing helix  chain 'A' and resid 168 through 189
      removed outlier: 3.718A  pdb=" N   ILE A 176 " --> pdb=" O   CYS A 172 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ILE A 179 " --> pdb=" O   SER A 175 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE A 185 " --> pdb=" O   PHE A 181 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   MET A 186 " --> pdb=" O   LEU A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 216
      removed outlier: 3.974A  pdb=" N   PHE A 199 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   CYS A 207 " --> pdb=" O   LEU A 203 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   TYR A 208 " --> pdb=" O   LEU A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 244
      removed outlier: 4.633A  pdb=" N   VAL A 222 " --> pdb=" O   GLN A 218 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA A 234 " --> pdb=" O   ILE A 230 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   VAL A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 258
      removed outlier: 4.099A  pdb=" N   LEU A 256 " --> pdb=" O   ASP A 252 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL A 258 " --> pdb=" O   HIS A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 275
      removed outlier: 3.904A  pdb=" N   MET A 262 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   THR A 266 " --> pdb=" O   MET A 262 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   SER A 267 " --> pdb=" O   ASN A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 307
      removed outlier: 3.912A  pdb=" N   ARG A 303 " --> pdb=" O   TYR A 299 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   SER A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   ALA A 305 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 313
    Processing helix  chain 'A' and resid 314 through 320
      removed outlier: 3.962A  pdb=" N   ILE A 320 " --> pdb=" O   MET A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 349
    Processing helix  chain 'A' and resid 350 through 361
      removed outlier: 3.922A  pdb=" N   ALA A 354 " --> pdb=" O   PHE A 350 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ILE A 359 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 371
    Processing helix  chain 'A' and resid 373 through 397
      removed outlier: 3.550A  pdb=" N   LEU A 388 " --> pdb=" O   GLY A 384 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   GLY A 392 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LYS A 397 " --> pdb=" O   GLU A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 424
      removed outlier: 4.029A  pdb=" N   LYS A 423 " --> pdb=" O   HIS A 419 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LYS A 424 " --> pdb=" O   LYS A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 536
    Processing helix  chain 'A' and resid 537 through 542
    Processing helix  chain 'A' and resid 544 through 565
      removed outlier: 3.896A  pdb=" N   GLN A 552 " --> pdb=" O   VAL A 548 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ASN A 553 " --> pdb=" O   ALA A 549 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   VAL A 554 " --> pdb=" O   ARG A 550 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   VAL A 555 " --> pdb=" O   LEU A 551 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASP A 556 " --> pdb=" O   GLN A 552 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   LEU A 561 " --> pdb=" O   ALA A 557 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 84
      removed outlier: 3.533A  pdb=" N   ASP B  72 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 109
    Processing helix  chain 'B' and resid 117 through 128
      removed outlier: 3.743A  pdb=" N   ALA B 121 " --> pdb=" O   TYR B 117 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE B 122 " --> pdb=" O   SER B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 163
    Processing helix  chain 'B' and resid 168 through 189
      removed outlier: 3.719A  pdb=" N   ILE B 176 " --> pdb=" O   CYS B 172 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ILE B 179 " --> pdb=" O   SER B 175 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE B 185 " --> pdb=" O   PHE B 181 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   MET B 186 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 216
      removed outlier: 3.974A  pdb=" N   PHE B 199 " --> pdb=" O   TYR B 195 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   CYS B 207 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   TYR B 208 " --> pdb=" O   LEU B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 218 through 244
      removed outlier: 4.633A  pdb=" N   VAL B 222 " --> pdb=" O   GLN B 218 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ALA B 234 " --> pdb=" O   ILE B 230 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   VAL B 236 " --> pdb=" O   LEU B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 258
      removed outlier: 4.099A  pdb=" N   LEU B 256 " --> pdb=" O   ASP B 252 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL B 258 " --> pdb=" O   HIS B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 275
      removed outlier: 3.904A  pdb=" N   MET B 262 " --> pdb=" O   VAL B 258 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   THR B 266 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   SER B 267 " --> pdb=" O   ASN B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 307
      removed outlier: 3.912A  pdb=" N   ARG B 303 " --> pdb=" O   TYR B 299 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   SER B 304 " --> pdb=" O   LYS B 300 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   ALA B 305 " --> pdb=" O   GLY B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 313
    Processing helix  chain 'B' and resid 314 through 320
      removed outlier: 3.962A  pdb=" N   ILE B 320 " --> pdb=" O   MET B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 349
    Processing helix  chain 'B' and resid 350 through 361
      removed outlier: 3.921A  pdb=" N   ALA B 354 " --> pdb=" O   PHE B 350 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ILE B 359 " --> pdb=" O   LEU B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 371
    Processing helix  chain 'B' and resid 373 through 397
      removed outlier: 3.550A  pdb=" N   LEU B 388 " --> pdb=" O   GLY B 384 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLY B 392 " --> pdb=" O   LEU B 388 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LYS B 397 " --> pdb=" O   GLU B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 424
      removed outlier: 4.028A  pdb=" N   LYS B 423 " --> pdb=" O   HIS B 419 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS B 424 " --> pdb=" O   LYS B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 542
      removed outlier: 3.650A  pdb=" N   ALA B 538 " --> pdb=" O   ALA B 534 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA B 541 " --> pdb=" O   LEU B 537 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 565
      removed outlier: 3.895A  pdb=" N   GLN B 552 " --> pdb=" O   VAL B 548 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ASN B 553 " --> pdb=" O   ALA B 549 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   VAL B 554 " --> pdb=" O   ARG B 550 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   VAL B 555 " --> pdb=" O   LEU B 551 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASP B 556 " --> pdb=" O   GLN B 552 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   LEU B 561 " --> pdb=" O   ALA B 557 " (cutoff:3.500A)

    391 hydrogen bonds defined for protein.
    1170 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: 0.71

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.03 -     1.18: 32
        1.18 -     1.34: 1845
        1.34 -     1.50: 1759
        1.50 -     1.65: 2388
        1.65 -     1.81: 50
  Bond restraints: 6074
  Sorted by residual:
  bond pdb=" C   VAL A 125 "
       pdb=" O   VAL A 125 "
    ideal  model  delta    sigma   weight residual
    1.237  1.027  0.210 1.19e-02 7.06e+03 3.12e+02
  bond pdb=" C   VAL B 125 "
       pdb=" O   VAL B 125 "
    ideal  model  delta    sigma   weight residual
    1.237  1.027  0.210 1.19e-02 7.06e+03 3.12e+02
  bond pdb=" CA  PHE A 540 "
       pdb=" C   PHE A 540 "
    ideal  model  delta    sigma   weight residual
    1.521  1.359  0.161 9.90e-03 1.02e+04 2.66e+02
  bond pdb=" CA  TRP A 120 "
       pdb=" C   TRP A 120 "
    ideal  model  delta    sigma   weight residual
    1.524  1.321  0.203 1.27e-02 6.20e+03 2.54e+02
  bond pdb=" CA  TRP B 120 "
       pdb=" C   TRP B 120 "
    ideal  model  delta    sigma   weight residual
    1.524  1.321  0.203 1.27e-02 6.20e+03 2.54e+02
  ... (remaining 6069 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.63: 8061
        5.63 -    11.26: 134
       11.26 -    16.90: 27
       16.90 -    22.53: 4
       22.53 -    28.16: 3
  Bond angle restraints: 8229
  Sorted by residual:
  angle pdb=" N   LEU B 114 "
        pdb=" CA  LEU B 114 "
        pdb=" C   LEU B 114 "
      ideal   model   delta    sigma   weight residual
     110.61  134.53  -23.92 1.25e+00 6.40e-01 3.66e+02
  angle pdb=" N   LEU A 114 "
        pdb=" CA  LEU A 114 "
        pdb=" C   LEU A 114 "
      ideal   model   delta    sigma   weight residual
     110.61  134.47  -23.86 1.25e+00 6.40e-01 3.64e+02
  angle pdb=" CA  THR B 539 "
        pdb=" C   THR B 539 "
        pdb=" N   PHE B 540 "
      ideal   model   delta    sigma   weight residual
     118.08  136.86  -18.78 1.30e+00 5.92e-01 2.09e+02
  angle pdb=" CA  VAL A 119 "
        pdb=" C   VAL A 119 "
        pdb=" N   TRP A 120 "
      ideal   model   delta    sigma   weight residual
     117.89  131.62  -13.73 1.34e+00 5.57e-01 1.05e+02
  angle pdb=" CA  VAL B 119 "
        pdb=" C   VAL B 119 "
        pdb=" N   TRP B 120 "
      ideal   model   delta    sigma   weight residual
     118.25  131.61  -13.36 1.33e+00 5.65e-01 1.01e+02
  ... (remaining 8224 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.82: 3086
       16.82 -    33.64: 361
       33.64 -    50.47: 97
       50.47 -    67.29: 11
       67.29 -    84.11: 8
  Dihedral angle restraints: 3563
    sinusoidal: 1337
      harmonic: 2226
  Sorted by residual:
  dihedral pdb=" C   SER B 118 "
           pdb=" N   SER B 118 "
           pdb=" CA  SER B 118 "
           pdb=" CB  SER B 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -160.35   37.75     0      2.50e+00 1.60e-01 2.28e+02
  dihedral pdb=" C   SER A 118 "
           pdb=" N   SER A 118 "
           pdb=" CA  SER A 118 "
           pdb=" CB  SER A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -160.12   37.52     0      2.50e+00 1.60e-01 2.25e+02
  dihedral pdb=" N   SER B 118 "
           pdb=" C   SER B 118 "
           pdb=" CA  SER B 118 "
           pdb=" CB  SER B 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  159.33  -36.53     0      2.50e+00 1.60e-01 2.13e+02
  ... (remaining 3560 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.353: 906
       0.353 -    0.706: 29
       0.706 -    1.059: 6
       1.059 -    1.412: 1
       1.412 -    1.765: 2
  Chirality restraints: 944
  Sorted by residual:
  chirality pdb=" CA  SER B 118 "
            pdb=" N   SER B 118 "
            pdb=" C   SER B 118 "
            pdb=" CB  SER B 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.75    1.77 2.00e-01 2.50e+01 7.79e+01
  chirality pdb=" CA  SER A 118 "
            pdb=" N   SER A 118 "
            pdb=" C   SER A 118 "
            pdb=" CB  SER A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.75    1.76 2.00e-01 2.50e+01 7.71e+01
  chirality pdb=" CA  LEU B 535 "
            pdb=" N   LEU B 535 "
            pdb=" C   LEU B 535 "
            pdb=" CB  LEU B 535 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.44    1.07 2.00e-01 2.50e+01 2.89e+01
  ... (remaining 941 not shown)

  Planarity restraints: 1021
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 113 "    0.042 2.00e-02 2.50e+03   8.42e-02 7.10e+01
        pdb=" C   ASP B 113 "   -0.146 2.00e-02 2.50e+03
        pdb=" O   ASP B 113 "    0.058 2.00e-02 2.50e+03
        pdb=" N   LEU B 114 "    0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 113 "   -0.042 2.00e-02 2.50e+03   8.41e-02 7.08e+01
        pdb=" C   ASP A 113 "    0.145 2.00e-02 2.50e+03
        pdb=" O   ASP A 113 "   -0.058 2.00e-02 2.50e+03
        pdb=" N   LEU A 114 "   -0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 540 "    0.098 2.00e-02 2.50e+03   6.31e-02 6.96e+01
        pdb=" CG  PHE B 540 "   -0.118 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 540 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 540 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 540 "    0.025 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 540 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 540 "    0.044 2.00e-02 2.50e+03
  ... (remaining 1018 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 132
        2.61 -     3.19: 5629
        3.19 -     3.76: 9032
        3.76 -     4.33: 12665
        4.33 -     4.90: 20360
  Nonbonded interactions: 47818
  Sorted by model distance:
  nonbonded pdb=" O   THR A 539 "
            pdb=" OG1 THR A 539 "
     model   vdw
     2.043 3.040
  nonbonded pdb=" OH  TYR B 208 "
            pdb=" NH1 ARG B 226 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" OH  TYR A 208 "
            pdb=" NH1 ARG A 226 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" O   THR B 539 "
            pdb=" OG1 THR B 539 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   ARG B 116 "
            pdb=" CA  TYR B 117 "
     model   vdw
     2.234 2.776
  ... (remaining 47813 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'
  selection = (chain 'B' and resid 67 through 565)
}

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=0.50 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:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.650
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6763
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      :  0.023   0.294   6074  Z= 1.535
  Angle     :  1.698  28.160   8229  Z= 1.090
  Chirality :  0.154   1.765    944
  Planarity :  0.009   0.084   1021
  Dihedral  : 15.839  84.110   2131
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 23.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  2.13 %
    Favored  : 96.07 %
  Cbeta Deviations :  3.91 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.99 (0.26), residues: 752
  helix: -2.16 (0.18), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.83 (0.47), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 379 
 TYR   0.072   0.003   TYR A 117 
 PHE   0.118   0.005   PHE B 540 
 TRP   0.025   0.003   TRP B 120 
 HIS   0.002   0.001   HIS A 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.02320 ( 6074)
  covalent geometry    : angle       1.69779 ( 8229)
  hydrogen bonds       : bond        0.23706 (  391)
  hydrogen bonds       : angle       9.99663 ( 1170)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A  115 SER cc_start: 0.6266 (OUTLIER) cc_final: 0.5350 (t)
REVERT: A  116 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6957 (ptt-90)
REVERT: B  115 SER cc_start: 0.6267 (OUTLIER) cc_final: 0.5323 (t)
REVERT: B  116 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6925 (ptt-90)
REVERT: B  181 PHE cc_start: 0.8367 (t80) cc_final: 0.8077 (t80)
REVERT: B  424 LYS cc_start: 0.8650 (mtmt) cc_final: 0.8360 (mtmm)
REVERT: B  537 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7765 (tp)
  outliers start: 11
  outliers final: 6
  residues processed: 97
  average time/residue: 0.0893
  time to fit residues: 10.8166
Evaluate side-chains
  88 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  116 ARG
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  116 ARG
Chi-restraints excluded: chain B residue  117 TYR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  537 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0870
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:   40.0000
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
A 356 HIS
B 241 ASN
B 356 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.197802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.176111 restraints weight = 6520.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3961 rms_B_bonded: 1.63
r_work: 0.3869 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3717 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3704
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3704 r_free = 0.3704    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3703 r_free = 0.3703    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3703
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6718
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6074  Z= 0.157
  Angle     :  0.629   8.276   8229  Z= 0.335
  Chirality :  0.039   0.149    944
  Planarity :  0.005   0.041   1021
  Dihedral  :  7.945  57.889    847
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 10.00 %
    Favored  : 88.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.24 (0.29), residues: 752
  helix: -0.96 (0.20), residues: 584
  sheet:  None (None), residues: 0
  loop : -2.88 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 374 
 TYR   0.016   0.001   TYR B 117 
 PHE   0.013   0.001   PHE A 181 
 TRP   0.004   0.001   TRP A 248 
 HIS   0.015   0.002   HIS B 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6074)
  covalent geometry    : angle       0.62870 ( 8229)
  hydrogen bonds       : bond        0.05056 (  391)
  hydrogen bonds       : angle       5.62175 ( 1170)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  186 MET cc_start: 0.5351 (mtm) cc_final: 0.5018 (mtm)
REVERT: A  535 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8186 (tt)
REVERT: B  181 PHE cc_start: 0.8345 (t80) cc_final: 0.8094 (t80)
REVERT: B  186 MET cc_start: 0.5426 (mtm) cc_final: 0.5088 (mtm)
REVERT: B  408 PHE cc_start: 0.8413 (t80) cc_final: 0.8113 (t80)
  outliers start: 12
  outliers final: 9
  residues processed: 107
  average time/residue: 0.0768
  time to fit residues: 10.7683
Evaluate side-chains
  98 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  185 PHE
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain B residue  117 TYR
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  175 SER
Chi-restraints excluded: chain B residue  185 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 39 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 21 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4160 r_free = 0.4160 target = 0.199061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.176710 restraints weight = 6483.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3955 rms_B_bonded: 1.65
r_work: 0.3865 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3714 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3719
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3719 r_free = 0.3719    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3719 r_free = 0.3719    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3719
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6670
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6074  Z= 0.148
  Angle     :  0.567   7.229   8229  Z= 0.302
  Chirality :  0.038   0.132    944
  Planarity :  0.004   0.040   1021
  Dihedral  :  6.303  55.153    833
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.41 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.30), residues: 752
  helix: -0.26 (0.21), residues: 582
  sheet:  None (None), residues: 0
  loop : -2.73 (0.49), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 374 
 TYR   0.010   0.001   TYR B 117 
 PHE   0.011   0.001   PHE A 547 
 TRP   0.007   0.001   TRP B 167 
 HIS   0.003   0.001   HIS B 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6074)
  covalent geometry    : angle       0.56691 ( 8229)
  hydrogen bonds       : bond        0.04473 (  391)
  hydrogen bonds       : angle       5.00465 ( 1170)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  157 MET cc_start: 0.6637 (tpp) cc_final: 0.6238 (tpp)
REVERT: A  186 MET cc_start: 0.5984 (mtm) cc_final: 0.5496 (mtm)
REVERT: A  196 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7433 (tm-30)
REVERT: B  116 ARG cc_start: 0.6419 (ptm-80) cc_final: 0.5788 (ttp80)
REVERT: B  157 MET cc_start: 0.6626 (tpp) cc_final: 0.6211 (tpp)
REVERT: B  186 MET cc_start: 0.6018 (mtm) cc_final: 0.5486 (mtm)
REVERT: B  196 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7498 (tm-30)
REVERT: B  371 GLN cc_start: 0.7232 (mp10) cc_final: 0.6892 (mp10)
  outliers start: 15
  outliers final: 13
  residues processed: 98
  average time/residue: 0.0877
  time to fit residues: 11.3261
Evaluate side-chains
  99 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  172 CYS
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  185 PHE
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain B residue  117 TYR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  172 CYS
Chi-restraints excluded: chain B residue  175 SER
Chi-restraints excluded: chain B residue  185 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 57 optimal weight:    0.3980
   chunk 53 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 0 optimal weight:   40.0000
   chunk 65 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0980
   chunk 12 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0980
   overall best weight:    0.3980

-------------------------------------------------------------------------------
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 = 0.4318 r_free = 0.4318 target = 0.209444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.184831 restraints weight = 6550.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.4085 rms_B_bonded: 2.02
r_work: 0.3971 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3972
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3972 r_free = 0.3972    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3972 r_free = 0.3972    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3972
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6575
moved from start:          0.3321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6074  Z= 0.116
  Angle     :  0.506   6.565   8229  Z= 0.270
  Chirality :  0.037   0.122    944
  Planarity :  0.004   0.038   1021
  Dihedral  :  5.841  51.732    831
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 16.56 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.31), residues: 752
  helix:  0.26 (0.21), residues: 584
  sheet:  None (None), residues: 0
  loop : -2.80 (0.48), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 374 
 TYR   0.009   0.001   TYR B 302 
 PHE   0.013   0.001   PHE B 408 
 TRP   0.009   0.001   TRP B 167 
 HIS   0.002   0.001   HIS A 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6074)
  covalent geometry    : angle       0.50571 ( 8229)
  hydrogen bonds       : bond        0.03922 (  391)
  hydrogen bonds       : angle       4.55291 ( 1170)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A  116 ARG cc_start: 0.6352 (ptm-80) cc_final: 0.5725 (ttp80)
REVERT: A  196 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7454 (tm-30)
REVERT: A  252 ASP cc_start: 0.8202 (t0) cc_final: 0.7907 (t0)
REVERT: A  388 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6191 (tt)
REVERT: A  415 GLU cc_start: 0.7550 (tm-30) cc_final: 0.6854 (tm-30)
REVERT: B  116 ARG cc_start: 0.6345 (ptm-80) cc_final: 0.5885 (ttp80)
REVERT: B  196 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7552 (tm-30)
REVERT: B  371 GLN cc_start: 0.7295 (mp10) cc_final: 0.7029 (mp10)
REVERT: B  388 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6219 (tt)
REVERT: B  415 GLU cc_start: 0.7620 (tm-30) cc_final: 0.6951 (tm-30)
  outliers start: 24
  outliers final: 10
  residues processed: 105
  average time/residue: 0.0806
  time to fit residues: 10.9891
Evaluate side-chains
  92 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain B residue  117 TYR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  175 SER
Chi-restraints excluded: chain B residue  388 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0570
   chunk 46 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0270
   overall best weight:    0.4156

-------------------------------------------------------------------------------
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 = 0.4320 r_free = 0.4320 target = 0.209046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.184035 restraints weight = 6651.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 2.08
r_work: 0.3966 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3966
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3966 r_free = 0.3966    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3966 r_free = 0.3966    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3966
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6586
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6074  Z= 0.117
  Angle     :  0.511   7.109   8229  Z= 0.266
  Chirality :  0.037   0.127    944
  Planarity :  0.003   0.038   1021
  Dihedral  :  5.334  49.856    829
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.38 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.31), residues: 752
  helix:  0.52 (0.22), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.71 (0.50), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 374 
 TYR   0.010   0.001   TYR B 302 
 PHE   0.009   0.001   PHE A 219 
 TRP   0.008   0.001   TRP A 167 
 HIS   0.002   0.001   HIS A 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6074)
  covalent geometry    : angle       0.51123 ( 8229)
  hydrogen bonds       : bond        0.03782 (  391)
  hydrogen bonds       : angle       4.38901 ( 1170)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  116 ARG cc_start: 0.6398 (ptm-80) cc_final: 0.5883 (ttp80)
REVERT: A  117 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6364 (p90)
REVERT: A  196 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7496 (tm-30)
REVERT: A  252 ASP cc_start: 0.8215 (t0) cc_final: 0.7957 (t0)
REVERT: A  388 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6251 (tt)
REVERT: A  415 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6774 (tm-30)
REVERT: B  116 ARG cc_start: 0.6392 (ptm-80) cc_final: 0.5926 (ttp80)
REVERT: B  117 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6683 (p90)
REVERT: B  186 MET cc_start: 0.5995 (mtm) cc_final: 0.5426 (mtm)
REVERT: B  196 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7529 (tm-30)
REVERT: B  252 ASP cc_start: 0.8170 (t0) cc_final: 0.7866 (t0)
REVERT: B  371 GLN cc_start: 0.7272 (mp10) cc_final: 0.6860 (mp10)
REVERT: B  388 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6250 (tt)
REVERT: B  415 GLU cc_start: 0.7489 (tm-30) cc_final: 0.6845 (tm-30)
  outliers start: 20
  outliers final: 9
  residues processed: 94
  average time/residue: 0.0907
  time to fit residues: 11.1134
Evaluate side-chains
  94 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  185 PHE
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  117 TYR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  175 SER
Chi-restraints excluded: chain B residue  185 PHE
Chi-restraints excluded: chain B residue  388 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4304 r_free = 0.4304 target = 0.207131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.182034 restraints weight = 6578.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.4040 rms_B_bonded: 2.08
r_work: 0.3928 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3930 r_free = 0.3930    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3930 r_free = 0.3930    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6641
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6074  Z= 0.149
  Angle     :  0.538   7.401   8229  Z= 0.282
  Chirality :  0.038   0.139    944
  Planarity :  0.004   0.038   1021
  Dihedral  :  5.365  46.962    829
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 19.67 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.32), residues: 752
  helix:  0.45 (0.21), residues: 602
  sheet:  None (None), residues: 0
  loop : -2.55 (0.54), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 374 
 TYR   0.009   0.001   TYR B 302 
 PHE   0.016   0.001   PHE A 199 
 TRP   0.009   0.001   TRP B 120 
 HIS   0.002   0.001   HIS B 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6074)
  covalent geometry    : angle       0.53762 ( 8229)
  hydrogen bonds       : bond        0.04122 (  391)
  hydrogen bonds       : angle       4.49048 ( 1170)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  117 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6656 (p90)
REVERT: A  196 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7457 (tm-30)
REVERT: A  252 ASP cc_start: 0.8249 (t0) cc_final: 0.8046 (t0)
REVERT: A  387 LEU cc_start: 0.7025 (tt) cc_final: 0.6503 (tp)
REVERT: A  388 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6638 (tt)
REVERT: B  116 ARG cc_start: 0.6537 (ptm-80) cc_final: 0.5934 (ttp80)
REVERT: B  117 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6742 (p90)
REVERT: B  186 MET cc_start: 0.6187 (mtm) cc_final: 0.5892 (mtm)
REVERT: B  196 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7527 (tm-30)
REVERT: B  252 ASP cc_start: 0.8198 (t0) cc_final: 0.7942 (t0)
REVERT: B  387 LEU cc_start: 0.7028 (tt) cc_final: 0.6304 (tp)
REVERT: B  388 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6642 (tt)
REVERT: B  415 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6719 (tm-30)
  outliers start: 19
  outliers final: 11
  residues processed: 98
  average time/residue: 0.0761
  time to fit residues: 9.8735
Evaluate side-chains
  92 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  172 CYS
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  185 PHE
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  117 TYR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  172 CYS
Chi-restraints excluded: chain B residue  175 SER
Chi-restraints excluded: chain B residue  185 PHE
Chi-restraints excluded: chain B residue  388 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 0 optimal weight:   40.0000
   chunk 32 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 24 optimal weight:    0.2980
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4299 r_free = 0.4299 target = 0.206806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.182316 restraints weight = 6598.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.4057 rms_B_bonded: 2.04
r_work: 0.3945 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3945
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3945 r_free = 0.3945    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3945 r_free = 0.3945    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3945
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6649
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6074  Z= 0.134
  Angle     :  0.523   7.415   8229  Z= 0.274
  Chirality :  0.037   0.138    944
  Planarity :  0.003   0.038   1021
  Dihedral  :  5.259  43.896    829
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.82 %
    Favored  : 76.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.32), residues: 752
  helix:  0.56 (0.22), residues: 604
  sheet:  None (None), residues: 0
  loop : -2.76 (0.52), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 374 
 TYR   0.009   0.001   TYR B 302 
 PHE   0.013   0.001   PHE A 199 
 TRP   0.010   0.001   TRP B 167 
 HIS   0.002   0.001   HIS B 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6074)
  covalent geometry    : angle       0.52258 ( 8229)
  hydrogen bonds       : bond        0.03937 (  391)
  hydrogen bonds       : angle       4.37502 ( 1170)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A  116 ARG cc_start: 0.6550 (ptm-80) cc_final: 0.5968 (ttp80)
REVERT: A  117 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6765 (p90)
REVERT: A  196 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7500 (tm-30)
REVERT: A  387 LEU cc_start: 0.7072 (tt) cc_final: 0.6504 (tp)
REVERT: A  388 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6683 (tt)
REVERT: B  116 ARG cc_start: 0.6497 (ptm-80) cc_final: 0.6150 (ttp80)
REVERT: B  117 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6891 (p90)
REVERT: B  252 ASP cc_start: 0.8164 (t0) cc_final: 0.7921 (t0)
REVERT: B  371 GLN cc_start: 0.7646 (mp10) cc_final: 0.7086 (mp10)
REVERT: B  387 LEU cc_start: 0.7057 (tt) cc_final: 0.6370 (tp)
REVERT: B  388 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6714 (tt)
REVERT: B  415 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6739 (tm-30)
  outliers start: 19
  outliers final: 11
  residues processed: 92
  average time/residue: 0.0806
  time to fit residues: 9.7376
Evaluate side-chains
  93 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  185 PHE
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  117 TYR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  172 CYS
Chi-restraints excluded: chain B residue  175 SER
Chi-restraints excluded: chain B residue  185 PHE
Chi-restraints excluded: chain B residue  388 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 1 optimal weight:   20.0000
   chunk 6 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4287 r_free = 0.4287 target = 0.205395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.180732 restraints weight = 6571.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.4044 rms_B_bonded: 2.02
r_work: 0.3933 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3935
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3935 r_free = 0.3935    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3935 r_free = 0.3935    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3935
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6675
moved from start:          0.3744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6074  Z= 0.148
  Angle     :  0.535   7.680   8229  Z= 0.282
  Chirality :  0.038   0.143    944
  Planarity :  0.004   0.038   1021
  Dihedral  :  5.286  42.048    829
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 20.82 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.32), residues: 752
  helix:  0.56 (0.21), residues: 604
  sheet:  None (None), residues: 0
  loop : -2.58 (0.54), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 374 
 TYR   0.010   0.001   TYR B 195 
 PHE   0.017   0.001   PHE A 199 
 TRP   0.009   0.001   TRP B 120 
 HIS   0.002   0.001   HIS B 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6074)
  covalent geometry    : angle       0.53505 ( 8229)
  hydrogen bonds       : bond        0.04090 (  391)
  hydrogen bonds       : angle       4.41874 ( 1170)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  115 SER cc_start: 0.6766 (p) cc_final: 0.6474 (t)
REVERT: A  117 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6922 (p90)
REVERT: A  196 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7542 (tm-30)
REVERT: A  387 LEU cc_start: 0.7096 (tt) cc_final: 0.6582 (tp)
REVERT: A  388 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6666 (tt)
REVERT: B  116 ARG cc_start: 0.6657 (ptm-80) cc_final: 0.6238 (ttp80)
REVERT: B  117 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6895 (p90)
REVERT: B  252 ASP cc_start: 0.8157 (t0) cc_final: 0.7939 (t0)
REVERT: B  387 LEU cc_start: 0.7071 (tt) cc_final: 0.6569 (tp)
REVERT: B  388 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6729 (tt)
REVERT: B  563 GLN cc_start: 0.6204 (OUTLIER) cc_final: 0.5985 (pt0)
  outliers start: 20
  outliers final: 14
  residues processed: 94
  average time/residue: 0.0849
  time to fit residues: 10.3516
Evaluate side-chains
  93 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 MET
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  172 CYS
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  185 PHE
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  117 TYR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  172 CYS
Chi-restraints excluded: chain B residue  175 SER
Chi-restraints excluded: chain B residue  185 PHE
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  563 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0870
   chunk 73 optimal weight:    1.9990
   chunk 48 optimal weight:    0.3980
   chunk 38 optimal weight:   30.0000
   chunk 66 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 57 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   overall best weight:    0.4558

-------------------------------------------------------------------------------
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 = 0.4316 r_free = 0.4316 target = 0.208517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.183542 restraints weight = 6590.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 2.12
r_work: 0.3957 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3956
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3956 r_free = 0.3956    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3956 r_free = 0.3956    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3956
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6581
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6074  Z= 0.118
  Angle     :  0.516   7.218   8229  Z= 0.267
  Chirality :  0.037   0.133    944
  Planarity :  0.003   0.037   1021
  Dihedral  :  5.120  40.238    829
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.82 %
    Favored  : 75.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.32), residues: 752
  helix:  0.87 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.74 (0.51), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 374 
 TYR   0.009   0.001   TYR B 302 
 PHE   0.014   0.001   PHE A 199 
 TRP   0.010   0.001   TRP A 167 
 HIS   0.002   0.000   HIS A 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6074)
  covalent geometry    : angle       0.51571 ( 8229)
  hydrogen bonds       : bond        0.03720 (  391)
  hydrogen bonds       : angle       4.21565 ( 1170)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  115 SER cc_start: 0.6732 (p) cc_final: 0.6448 (t)
REVERT: A  117 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6928 (p90)
REVERT: A  196 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7495 (tm-30)
REVERT: A  388 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6658 (tt)
REVERT: B  116 ARG cc_start: 0.6493 (ptm-80) cc_final: 0.5996 (ttp80)
REVERT: B  117 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.6835 (p90)
REVERT: B  252 ASP cc_start: 0.8129 (t0) cc_final: 0.7861 (t0)
REVERT: B  371 GLN cc_start: 0.7592 (mp10) cc_final: 0.7031 (mp10)
REVERT: B  387 LEU cc_start: 0.6954 (tt) cc_final: 0.6086 (tp)
REVERT: B  388 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6635 (tt)
REVERT: B  563 GLN cc_start: 0.6249 (OUTLIER) cc_final: 0.5928 (pt0)
  outliers start: 21
  outliers final: 13
  residues processed: 95
  average time/residue: 0.0945
  time to fit residues: 11.7508
Evaluate side-chains
  92 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  172 CYS
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  185 PHE
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  117 TYR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  172 CYS
Chi-restraints excluded: chain B residue  175 SER
Chi-restraints excluded: chain B residue  185 PHE
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  563 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 21 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4282 r_free = 0.4282 target = 0.205489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.180260 restraints weight = 6615.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.4051 rms_B_bonded: 2.13
r_work: 0.3941 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3939
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3939 r_free = 0.3939    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3939 r_free = 0.3939    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3939
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6605
moved from start:          0.4040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6074  Z= 0.130
  Angle     :  0.527   7.423   8229  Z= 0.274
  Chirality :  0.037   0.139    944
  Planarity :  0.003   0.037   1021
  Dihedral  :  5.120  38.738    829
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 22.46 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.32), residues: 752
  helix:  0.86 (0.22), residues: 602
  sheet:  None (None), residues: 0
  loop : -2.73 (0.51), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 374 
 TYR   0.009   0.001   TYR B 302 
 PHE   0.016   0.001   PHE A 199 
 TRP   0.010   0.001   TRP A 167 
 HIS   0.002   0.001   HIS B 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6074)
  covalent geometry    : angle       0.52700 ( 8229)
  hydrogen bonds       : bond        0.03829 (  391)
  hydrogen bonds       : angle       4.23557 ( 1170)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A  115 SER cc_start: 0.6836 (p) cc_final: 0.6584 (t)
REVERT: A  117 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6987 (p90)
REVERT: A  196 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7512 (tm-30)
REVERT: A  388 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6695 (tt)
REVERT: B  100 ILE cc_start: 0.6108 (OUTLIER) cc_final: 0.5859 (tp)
REVERT: B  117 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6754 (p90)
REVERT: B  203 LEU cc_start: 0.7547 (tp) cc_final: 0.7319 (tt)
REVERT: B  252 ASP cc_start: 0.8150 (t0) cc_final: 0.7914 (t0)
REVERT: B  387 LEU cc_start: 0.6906 (tt) cc_final: 0.6431 (tp)
REVERT: B  388 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6295 (tt)
REVERT: B  563 GLN cc_start: 0.6209 (OUTLIER) cc_final: 0.5914 (pt0)
  outliers start: 19
  outliers final: 13
  residues processed: 88
  average time/residue: 0.0786
  time to fit residues: 9.3876
Evaluate side-chains
  90 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  172 CYS
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  185 PHE
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  117 TYR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  172 CYS
Chi-restraints excluded: chain B residue  175 SER
Chi-restraints excluded: chain B residue  185 PHE
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  563 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0870
   chunk 64 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 6 optimal weight:    0.2980
   chunk 29 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.4958

-------------------------------------------------------------------------------
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 = 0.4296 r_free = 0.4296 target = 0.206941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.181264 restraints weight = 6642.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 2.19
r_work: 0.3950 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3947 r_free = 0.3947    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3947 r_free = 0.3947    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6562
moved from start:          0.4129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6074  Z= 0.120
  Angle     :  0.515   7.143   8229  Z= 0.267
  Chirality :  0.037   0.135    944
  Planarity :  0.003   0.037   1021
  Dihedral  :  5.031  37.345    829
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 22.46 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.32), residues: 752
  helix:  0.96 (0.22), residues: 604
  sheet:  None (None), residues: 0
  loop : -2.73 (0.52), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 374 
 TYR   0.009   0.001   TYR B 302 
 PHE   0.015   0.001   PHE A 199 
 TRP   0.011   0.001   TRP A 167 
 HIS   0.002   0.001   HIS A 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6074)
  covalent geometry    : angle       0.51453 ( 8229)
  hydrogen bonds       : bond        0.03677 (  391)
  hydrogen bonds       : angle       4.13413 ( 1170)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1411.46 seconds
wall clock time: 24 minutes 57.18 seconds (1497.18 seconds total)