Starting phenix.real_space_refine
on Tue Feb  3 23:24:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p1k_13163/02_2026/7p1k_13163_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p1k_13163/02_2026/7p1k_13163.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p1k_13163/02_2026/7p1k_13163_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p1k_13163/02_2026/7p1k_13163_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p1k_13163/02_2026/7p1k_13163.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p1k_13163/02_2026/7p1k_13163.map"
  }
  resolution = 3.64
  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=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      38      5.16       5
     C    4648      2.51       5
     N    1032      2.21       5
     O    1170      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6892
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 3243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 433, 3243
          Classifications: {'peptide': 433}
          Link IDs: {'PTRANS': 19, 'TRANS': 413}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 3243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 433, 3243
          Classifications: {'peptide': 433}
          Link IDs: {'PTRANS': 19, 'TRANS': 413}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 203
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 203
          Unusual residues: {'T7X': 2, 'Y01': 4}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'T7X:plan-1': 1, 'T7X:plan-2': 1, 'T7X:plan-3': 1, 'T7X:plan-4': 1, 'T7X:plan-5': 1, 'T7X:plan-6': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "A"
      Number of atoms: 203
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 203
          Unusual residues: {'T7X': 2, 'Y01': 4}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'T7X:plan-1': 1, 'T7X:plan-2': 1, 'T7X:plan-3': 1, 'T7X:plan-4': 1, 'T7X:plan-5': 1, 'T7X:plan-6': 1}
          Unresolved non-hydrogen planarities: 24
  Time building chain proxies: 1.60, per 1000 atoms: 0.23
  Number of scatterers: 6892
  At special positions: 0
  Unit cell: (75.0915, 77.121, 118.726, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P       4     15.00
     O    1170      8.00
     N    1032      7.00
     C    4648      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: 0.75
  Conformation dependent library (CDL) restraints added in 272.7 milliseconds
  

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1536

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 0 sheets defined
      82.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'B' and resid 80 through 104
      removed outlier: 3.822A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  82 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LEU B  96 " --> pdb=" O   MET B  92 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   TRP B  97 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL B 103 " --> pdb=" O   VAL B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 134
      removed outlier: 3.704A  pdb=" N   GLY B 116 " --> pdb=" O   GLY B 112 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ILE B 117 " --> pdb=" O   ASN B 113 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   GLY B 132 " --> pdb=" O   GLY B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 158
      removed outlier: 4.342A  pdb=" N   GLY B 147 " --> pdb=" O   PRO B 143 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE B 155 " --> pdb=" O   ALA B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 162
      removed outlier: 3.811A  pdb=" N   SER B 162 " --> pdb=" O   PRO B 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 159 through 162'
    Processing helix  chain 'B' and resid 168 through 190
      removed outlier: 3.523A  pdb=" N   ILE B 183 " --> pdb=" O   ALA B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 199
      removed outlier: 3.509A  pdb=" N   LEU B 196 " --> pdb=" O   ASP B 192 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   LYS B 198 " --> pdb=" O   ASN B 194 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU B 199 " --> pdb=" O   ALA B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 226
      removed outlier: 3.709A  pdb=" N   VAL B 204 " --> pdb=" O   LYS B 200 " (cutoff:3.500A)
      Proline residue:  B 210  - end of helix
    Processing helix  chain 'B' and resid 229 through 241
      removed outlier: 3.573A  pdb=" N   PHE B 234 " --> pdb=" O   TRP B 230 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   MET B 235 " --> pdb=" O   GLN B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 259
      removed outlier: 3.922A  pdb=" N   VAL B 248 " --> pdb=" O   SER B 244 " (cutoff:3.500A)
      Proline residue:  B 250  - end of helix
    Processing helix  chain 'B' and resid 265 through 276
      removed outlier: 3.588A  pdb=" N   SER B 275 " --> pdb=" O   MET B 271 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   PHE B 276 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 293
      removed outlier: 3.665A  pdb=" N   ALA B 281 " --> pdb=" O   ASP B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 319
      removed outlier: 3.759A  pdb=" N   VAL B 309 " --> pdb=" O   GLY B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 357
      removed outlier: 3.741A  pdb=" N   ALA B 339 " --> pdb=" O   VAL B 335 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   PHE B 340 " --> pdb=" O   TRP B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 377
      removed outlier: 3.869A  pdb=" N   LEU B 364 " --> pdb=" O   GLY B 360 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU B 367 " --> pdb=" O   GLY B 363 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY B 376 " --> pdb=" O   LEU B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 404
      removed outlier: 3.608A  pdb=" N   LYS B 386 " --> pdb=" O   THR B 382 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   VAL B 387 " --> pdb=" O   ASP B 383 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL B 390 " --> pdb=" O   LYS B 386 " (cutoff:3.500A)
      Proline residue:  B 397  - end of helix
      removed outlier: 3.616A  pdb=" N   PHE B 400 " --> pdb=" O   GLN B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 439
      removed outlier: 3.572A  pdb=" N   VAL B 439 " --> pdb=" O   THR B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 455
      removed outlier: 3.796A  pdb=" N   ILE B 450 " --> pdb=" O   ILE B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 467
      removed outlier: 4.048A  pdb=" N   ALA B 464 " --> pdb=" O   ALA B 460 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA B 465 " --> pdb=" O   THR B 461 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ILE B 466 " --> pdb=" O   VAL B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 475
    Processing helix  chain 'B' and resid 480 through 516
      removed outlier: 4.179A  pdb=" N   GLY B 484 " --> pdb=" O   LYS B 480 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   TYR B 485 " --> pdb=" O   GLN B 481 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ILE B 497 " --> pdb=" O   ALA B 493 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ALA B 501 " --> pdb=" O   ILE B 497 " (cutoff:3.500A)
      Proline residue:  B 502  - end of helix
      removed outlier: 3.560A  pdb=" N   GLY B 509 " --> pdb=" O   SER B 505 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU B 510 " --> pdb=" O   LEU B 506 " (cutoff:3.500A)
      Proline residue:  B 513  - end of helix
      removed outlier: 3.884A  pdb=" N   LEU B 516 " --> pdb=" O   GLY B 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 104
      removed outlier: 3.792A  pdb=" N   LEU A  96 " --> pdb=" O   MET A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 131
      removed outlier: 3.543A  pdb=" N   ILE A 117 " --> pdb=" O   ASN A 113 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   PHE A 131 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 158
    Processing helix  chain 'A' and resid 159 through 162
      removed outlier: 3.559A  pdb=" N   SER A 162 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 159 through 162'
    Processing helix  chain 'A' and resid 168 through 190
      removed outlier: 3.527A  pdb=" N   ILE A 183 " --> pdb=" O   ALA A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 199
      removed outlier: 3.620A  pdb=" N   LEU A 196 " --> pdb=" O   ASP A 192 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LYS A 198 " --> pdb=" O   ASN A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 226
      removed outlier: 3.785A  pdb=" N   VAL A 204 " --> pdb=" O   LYS A 200 " (cutoff:3.500A)
      Proline residue:  A 210  - end of helix
    Processing helix  chain 'A' and resid 229 through 241
      removed outlier: 3.698A  pdb=" N   MET A 235 " --> pdb=" O   GLN A 231 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL A 239 " --> pdb=" O   MET A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 259
      removed outlier: 3.743A  pdb=" N   VAL A 248 " --> pdb=" O   SER A 244 " (cutoff:3.500A)
      Proline residue:  A 250  - end of helix
    Processing helix  chain 'A' and resid 265 through 276
      removed outlier: 3.566A  pdb=" N   SER A 275 " --> pdb=" O   MET A 271 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   PHE A 276 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 293
      removed outlier: 3.617A  pdb=" N   ALA A 281 " --> pdb=" O   ASP A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 321
      removed outlier: 3.691A  pdb=" N   VAL A 306 " --> pdb=" O   VAL A 302 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL A 309 " --> pdb=" O   GLY A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 357
      removed outlier: 3.500A  pdb=" N   ALA A 339 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE A 340 " --> pdb=" O   TRP A 336 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL A 342 " --> pdb=" O   ARG A 338 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR A 354 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 377
      removed outlier: 4.026A  pdb=" N   LEU A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   THR A 366 " --> pdb=" O   GLY A 362 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   LEU A 367 " --> pdb=" O   GLY A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 404
      removed outlier: 3.551A  pdb=" N   VAL A 384 " --> pdb=" O   THR A 380 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   LYS A 386 " --> pdb=" O   THR A 382 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL A 387 " --> pdb=" O   ASP A 383 " (cutoff:3.500A)
      Proline residue:  A 397  - end of helix
      removed outlier: 3.605A  pdb=" N   PHE A 400 " --> pdb=" O   GLN A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 438
    Processing helix  chain 'A' and resid 446 through 455
    Processing helix  chain 'A' and resid 460 through 466
      removed outlier: 4.056A  pdb=" N   ALA A 464 " --> pdb=" O   ALA A 460 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE A 466 " --> pdb=" O   VAL A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 477
    Processing helix  chain 'A' and resid 480 through 516
      removed outlier: 3.572A  pdb=" N   TYR A 485 " --> pdb=" O   GLN A 481 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ILE A 497 " --> pdb=" O   ALA A 493 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A 501 " --> pdb=" O   ILE A 497 " (cutoff:3.500A)
      Proline residue:  A 502  - end of helix
      removed outlier: 3.519A  pdb=" N   LEU A 510 " --> pdb=" O   LEU A 506 " (cutoff:3.500A)
      Proline residue:  A 513  - end of helix
      removed outlier: 3.854A  pdb=" N   LEU A 516 " --> pdb=" O   GLY A 512 " (cutoff:3.500A)

    449 hydrogen bonds defined for protein.
    1347 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: 0.90

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1015
        1.31 -     1.43: 1725
        1.43 -     1.56: 4156
        1.56 -     1.68: 104
        1.68 -     1.81: 56
  Bond restraints: 7056
  Sorted by residual:
  bond pdb=" C21 T7X A 806 "
       pdb=" C22 T7X A 806 "
    ideal  model  delta    sigma   weight residual
    1.329  1.528 -0.199 2.00e-02 2.50e+03 9.86e+01
  bond pdb=" C21 T7X B1203 "
       pdb=" C22 T7X B1203 "
    ideal  model  delta    sigma   weight residual
    1.329  1.527 -0.198 2.00e-02 2.50e+03 9.83e+01
  bond pdb=" C24 T7X A 806 "
       pdb=" C25 T7X A 806 "
    ideal  model  delta    sigma   weight residual
    1.330  1.527 -0.197 2.00e-02 2.50e+03 9.75e+01
  bond pdb=" C24 T7X B1203 "
       pdb=" C25 T7X B1203 "
    ideal  model  delta    sigma   weight residual
    1.330  1.527 -0.197 2.00e-02 2.50e+03 9.73e+01
  bond pdb=" C15 T7X B1203 "
       pdb=" C16 T7X B1203 "
    ideal  model  delta    sigma   weight residual
    1.332  1.528 -0.196 2.00e-02 2.50e+03 9.62e+01
  ... (remaining 7051 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.75: 9475
        3.75 -     7.50: 131
        7.50 -    11.26: 21
       11.26 -    15.01: 15
       15.01 -    18.76: 4
  Bond angle restraints: 9646
  Sorted by residual:
  angle pdb=" O11 T7X B1203 "
        pdb=" P1  T7X B1203 "
        pdb=" O12 T7X B1203 "
      ideal   model   delta    sigma   weight residual
     119.68  100.92   18.76 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" O11 T7X A 806 "
        pdb=" P1  T7X A 806 "
        pdb=" O12 T7X A 806 "
      ideal   model   delta    sigma   weight residual
     119.68  101.10   18.58 3.00e+00 1.11e-01 3.84e+01
  angle pdb=" N   ASP B 163 "
        pdb=" CA  ASP B 163 "
        pdb=" C   ASP B 163 "
      ideal   model   delta    sigma   weight residual
     114.31  106.98    7.33 1.29e+00 6.01e-01 3.23e+01
  angle pdb=" O1  T7X B1203 "
        pdb=" P1  T7X B1203 "
        pdb=" O13 T7X B1203 "
      ideal   model   delta    sigma   weight residual
      94.60  110.62  -16.02 3.00e+00 1.11e-01 2.85e+01
  angle pdb=" N   TRP B 171 "
        pdb=" CA  TRP B 171 "
        pdb=" C   TRP B 171 "
      ideal   model   delta    sigma   weight residual
     113.50  107.07    6.43 1.23e+00 6.61e-01 2.73e+01
  ... (remaining 9641 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.56: 4460
       35.56 -    71.11: 92
       71.11 -   106.67: 13
      106.67 -   142.22: 6
      142.22 -   177.78: 7
  Dihedral angle restraints: 4578
    sinusoidal: 2166
      harmonic: 2412
  Sorted by residual:
  dihedral pdb=" C7  T7X A 806 "
           pdb=" O13 T7X A 806 "
           pdb=" P1  T7X A 806 "
           pdb=" O12 T7X A 806 "
      ideal   model   delta sinusoidal    sigma   weight residual
      91.36  -90.86 -177.78     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C7  T7X B1203 "
           pdb=" O13 T7X B1203 "
           pdb=" P1  T7X B1203 "
           pdb=" O11 T7X B1203 "
      ideal   model   delta sinusoidal    sigma   weight residual
     318.06  147.62  170.44     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" C7  T7X B1203 "
           pdb=" O13 T7X B1203 "
           pdb=" P1  T7X B1203 "
           pdb=" O12 T7X B1203 "
      ideal   model   delta sinusoidal    sigma   weight residual
      91.36 -100.83 -167.81     1      3.00e+01 1.11e-03 2.11e+01
  ... (remaining 4575 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1112
       0.074 -    0.148: 59
       0.148 -    0.222: 23
       0.222 -    0.296: 2
       0.296 -    0.370: 8
  Chirality restraints: 1204
  Sorted by residual:
  chirality pdb=" CBG Y01 A 804 "
            pdb=" CAQ Y01 A 804 "
            pdb=" CBD Y01 A 804 "
            pdb=" CBI Y01 A 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.70    0.37 2.00e-01 2.50e+01 3.43e+00
  chirality pdb=" CBG Y01 B1201 "
            pdb=" CAQ Y01 B1201 "
            pdb=" CBD Y01 B1201 "
            pdb=" CBI Y01 B1201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.70    0.37 2.00e-01 2.50e+01 3.35e+00
  chirality pdb=" CBG Y01 A 803 "
            pdb=" CAQ Y01 A 803 "
            pdb=" CBD Y01 A 803 "
            pdb=" CBI Y01 A 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.69    0.36 2.00e-01 2.50e+01 3.18e+00
  ... (remaining 1201 not shown)

  Planarity restraints: 1118
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C17 T7X A 806 "    0.135 2.00e-02 2.50e+03   3.42e-01 1.17e+03
        pdb=" C18 T7X A 806 "   -0.438 2.00e-02 2.50e+03
        pdb=" C19 T7X A 806 "    0.476 2.00e-02 2.50e+03
        pdb=" C20 T7X A 806 "   -0.173 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C23 T7X A 806 "    0.150 2.00e-02 2.50e+03   3.31e-01 1.10e+03
        pdb=" C24 T7X A 806 "   -0.437 2.00e-02 2.50e+03
        pdb=" C25 T7X A 806 "    0.447 2.00e-02 2.50e+03
        pdb=" C26 T7X A 806 "   -0.159 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C23 T7X B1203 "   -0.152 2.00e-02 2.50e+03   3.11e-01 9.67e+02
        pdb=" C24 T7X B1203 "    0.410 2.00e-02 2.50e+03
        pdb=" C25 T7X B1203 "   -0.414 2.00e-02 2.50e+03
        pdb=" C26 T7X B1203 "    0.156 2.00e-02 2.50e+03
  ... (remaining 1115 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 52
        2.60 -     3.17: 6088
        3.17 -     3.75: 10006
        3.75 -     4.32: 13397
        4.32 -     4.90: 22515
  Nonbonded interactions: 52058
  Sorted by model distance:
  nonbonded pdb=" N   GLU A 385 "
            pdb=" OE1 GLU A 385 "
     model   vdw
     2.023 3.120
  nonbonded pdb=" O   PHE A 153 "
            pdb=" ND2 ASN A 157 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" O   PHE B 153 "
            pdb=" ND2 ASN B 157 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" O   PHE B 444 "
            pdb=" NZ  LYS B 449 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" O   VAL B 239 "
            pdb=" NE2 GLN B 463 "
     model   vdw
     2.304 3.120
  ... (remaining 52053 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 79 through 801 or resid 804))
  selection = (chain 'B' and (resid 79 through 1201 or resid 1204))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.610
  Find NCS groups from input model:        0.090
  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:0.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6864
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      :  0.014   0.199   7056  Z= 0.697
  Angle     :  1.119  18.761   9646  Z= 0.459
  Chirality :  0.053   0.370   1204
  Planarity :  0.024   0.342   1118
  Dihedral  : 16.196 177.778   3042
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  :  7.93 %
    Favored  : 87.46 %
  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 are not related in a simple way.
  whole: -0.19 (0.29), residues: 858
  helix:  0.60 (0.20), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.10 (0.46), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 186 
 TYR   0.005   0.001   TYR A 260 
 PHE   0.005   0.001   PHE A 300 
 TRP   0.020   0.001   TRP A 171 
 HIS   0.002   0.001   HIS A 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.01378 ( 7056)
  covalent geometry    : angle       1.11851 ( 9646)
  hydrogen bonds       : bond        0.29096 (  449)
  hydrogen bonds       : angle       6.94714 ( 1347)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 209
  time to evaluate  : 0.244 
Fit side-chains
TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it.
REVERT: B  200 LYS cc_start: 0.7652 (mtmt) cc_final: 0.7014 (mmtt)
REVERT: B  226 MET cc_start: 0.6218 (mmt) cc_final: 0.5976 (mpp)
REVERT: B  346 SER cc_start: 0.7929 (t) cc_final: 0.7727 (m)
REVERT: B  426 ILE cc_start: 0.8581 (mt) cc_final: 0.8376 (mm)
REVERT: B  438 MET cc_start: 0.7032 (mmm) cc_final: 0.6743 (mmt)
REVERT: B  507 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7748 (mt)
REVERT: A   86 VAL cc_start: 0.6782 (m) cc_final: 0.6572 (t)
REVERT: A   96 LEU cc_start: 0.8447 (tt) cc_final: 0.8125 (tp)
REVERT: A  165 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6990 (mt)
REVERT: A  396 GLN cc_start: 0.8563 (tp40) cc_final: 0.7649 (tt0)
  outliers start: 32
  outliers final: 9
  residues processed: 231
  average time/residue: 0.0838
  time to fit residues: 25.2443
Evaluate side-chains
  157 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  516 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  459 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.0970
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0670
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.4516

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

Flipped N/Q/H residues before XYZ refinement:
B 113 ASN
B 286 ASN
** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 477 HIS
A 113 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.204901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.174597 restraints weight = 7525.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.173826 restraints weight = 11216.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.173774 restraints weight = 11527.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.172885 restraints weight = 9068.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.173183 restraints weight = 8787.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6811
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7056  Z= 0.155
  Angle     :  0.718   8.923   9646  Z= 0.342
  Chirality :  0.041   0.168   1204
  Planarity :  0.005   0.045   1118
  Dihedral  : 16.696 175.872   1661
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 14.55 %
    Favored  : 81.84 %
  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 are not related in a simple way.
  whole:  1.09 (0.29), residues: 858
  helix:  1.65 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -2.25 (0.47), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 375 
 TYR   0.011   0.001   TYR A 223 
 PHE   0.013   0.001   PHE A 238 
 TRP   0.017   0.001   TRP A 171 
 HIS   0.002   0.001   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7056)
  covalent geometry    : angle       0.71761 ( 9646)
  hydrogen bonds       : bond        0.06612 (  449)
  hydrogen bonds       : angle       4.22749 ( 1347)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 0.170 
Fit side-chains
TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: B  200 LYS cc_start: 0.7527 (mtmt) cc_final: 0.7058 (mmtt)
REVERT: B  358 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.5729 (p90)
REVERT: B  388 ILE cc_start: 0.8943 (mt) cc_final: 0.8713 (mm)
REVERT: B  436 TYR cc_start: 0.7911 (t80) cc_final: 0.7530 (t80)
REVERT: A   96 LEU cc_start: 0.8032 (tt) cc_final: 0.7784 (tp)
REVERT: A  165 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7292 (mt)
REVERT: A  358 PHE cc_start: 0.7047 (m-80) cc_final: 0.6806 (m-10)
REVERT: A  396 GLN cc_start: 0.8636 (tp-100) cc_final: 0.7930 (tt0)
REVERT: A  495 LEU cc_start: 0.7617 (mt) cc_final: 0.7403 (mt)
  outliers start: 25
  outliers final: 15
  residues processed: 167
  average time/residue: 0.0832
  time to fit residues: 18.6256
Evaluate side-chains
  147 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  358 PHE
Chi-restraints excluded: chain B residue  462 VAL
Chi-restraints excluded: chain B residue  498 ILE
Chi-restraints excluded: chain B residue  516 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  498 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 82 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 84 optimal weight:    0.6980
   chunk 76 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
B 286 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.204257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.171033 restraints weight = 7618.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.170440 restraints weight = 11996.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.172441 restraints weight = 10391.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.168667 restraints weight = 8864.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.169574 restraints weight = 7735.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6899
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7056  Z= 0.168
  Angle     :  0.684   7.709   9646  Z= 0.327
  Chirality :  0.042   0.168   1204
  Planarity :  0.004   0.040   1118
  Dihedral  : 15.085 178.206   1653
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 13.98 %
    Favored  : 79.97 %
  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 are not related in a simple way.
  whole:  1.13 (0.29), residues: 858
  helix:  1.70 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.23 (0.45), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 156 
 TYR   0.012   0.002   TYR B 223 
 PHE   0.012   0.001   PHE A 153 
 TRP   0.010   0.001   TRP A 232 
 HIS   0.004   0.001   HIS B 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 7056)
  covalent geometry    : angle       0.68358 ( 9646)
  hydrogen bonds       : bond        0.06396 (  449)
  hydrogen bonds       : angle       4.13348 ( 1347)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 133
  time to evaluate  : 0.287 
Fit side-chains
TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: B   82 LEU cc_start: 0.4839 (OUTLIER) cc_final: 0.4487 (tp)
REVERT: B  200 LYS cc_start: 0.7693 (mtmt) cc_final: 0.6878 (mmtt)
REVERT: B  358 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.5660 (p90)
REVERT: B  436 TYR cc_start: 0.8054 (t80) cc_final: 0.7753 (t80)
REVERT: B  456 TRP cc_start: 0.8033 (OUTLIER) cc_final: 0.6838 (m-90)
REVERT: B  507 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7593 (mt)
REVERT: A   96 LEU cc_start: 0.7873 (tt) cc_final: 0.7645 (tp)
REVERT: A  396 GLN cc_start: 0.8604 (tp-100) cc_final: 0.7818 (tt0)
REVERT: A  495 LEU cc_start: 0.7663 (mt) cc_final: 0.7462 (mt)
REVERT: A  510 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6616 (pt)
  outliers start: 42
  outliers final: 25
  residues processed: 163
  average time/residue: 0.0845
  time to fit residues: 18.5227
Evaluate side-chains
  155 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  358 PHE
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  456 TRP
Chi-restraints excluded: chain B residue  462 VAL
Chi-restraints excluded: chain B residue  498 ILE
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  516 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  510 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0070
   chunk 47 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 53 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 82 optimal weight:   10.0000
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
B 286 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.202981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.167523 restraints weight = 7545.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.164968 restraints weight = 10429.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.167195 restraints weight = 11689.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.167038 restraints weight = 8088.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.167304 restraints weight = 7421.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6880
moved from start:          0.3630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7056  Z= 0.125
  Angle     :  0.630   8.922   9646  Z= 0.297
  Chirality :  0.039   0.165   1204
  Planarity :  0.004   0.043   1118
  Dihedral  : 13.925 178.581   1651
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 15.71 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.30), residues: 858
  helix:  1.87 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.09 (0.46), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 156 
 TYR   0.015   0.001   TYR A 485 
 PHE   0.010   0.001   PHE A 494 
 TRP   0.010   0.001   TRP A  97 
 HIS   0.004   0.001   HIS B 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7056)
  covalent geometry    : angle       0.63031 ( 9646)
  hydrogen bonds       : bond        0.04869 (  449)
  hydrogen bonds       : angle       3.84180 ( 1347)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 136
  time to evaluate  : 0.255 
Fit side-chains
TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: B   82 LEU cc_start: 0.4883 (OUTLIER) cc_final: 0.4531 (tp)
REVERT: B  200 LYS cc_start: 0.7628 (mtmt) cc_final: 0.6905 (mmtt)
REVERT: B  279 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.7809 (mp)
REVERT: B  358 PHE cc_start: 0.6664 (OUTLIER) cc_final: 0.5591 (p90)
REVERT: B  475 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7284 (ptp-110)
REVERT: B  477 HIS cc_start: 0.5673 (m-70) cc_final: 0.4981 (m-70)
REVERT: A  396 GLN cc_start: 0.8549 (tp-100) cc_final: 0.7839 (tt0)
REVERT: A  495 LEU cc_start: 0.7713 (mt) cc_final: 0.7493 (mt)
REVERT: A  510 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6613 (pt)
  outliers start: 31
  outliers final: 20
  residues processed: 156
  average time/residue: 0.0795
  time to fit residues: 16.8270
Evaluate side-chains
  155 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  358 PHE
Chi-restraints excluded: chain B residue  462 VAL
Chi-restraints excluded: chain B residue  498 ILE
Chi-restraints excluded: chain B residue  516 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  510 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 48 optimal weight:    0.1980
   chunk 44 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 59 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
B 286 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.198692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.164937 restraints weight = 7637.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.162810 restraints weight = 12024.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.164603 restraints weight = 12884.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.165045 restraints weight = 8967.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.165349 restraints weight = 9619.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7056  Z= 0.172
  Angle     :  0.671   6.824   9646  Z= 0.321
  Chirality :  0.042   0.189   1204
  Planarity :  0.004   0.039   1118
  Dihedral  : 13.225 177.587   1647
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 16.14 %
    Favored  : 78.96 %
  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 are not related in a simple way.
  whole:  1.13 (0.29), residues: 858
  helix:  1.68 (0.20), residues: 642
  sheet:  None (None), residues: 0
  loop : -2.19 (0.46), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 156 
 TYR   0.009   0.001   TYR B 260 
 PHE   0.015   0.001   PHE A 153 
 TRP   0.011   0.001   TRP A 232 
 HIS   0.005   0.001   HIS B 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 7056)
  covalent geometry    : angle       0.67056 ( 9646)
  hydrogen bonds       : bond        0.05886 (  449)
  hydrogen bonds       : angle       4.00029 ( 1347)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 0.244 
Fit side-chains
TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: B   82 LEU cc_start: 0.4881 (OUTLIER) cc_final: 0.4541 (tp)
REVERT: B  279 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.7816 (mp)
REVERT: B  358 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.5709 (p90)
REVERT: B  456 TRP cc_start: 0.8050 (OUTLIER) cc_final: 0.6981 (m-90)
REVERT: B  475 ARG cc_start: 0.7636 (ttm110) cc_final: 0.7380 (ptp-110)
REVERT: B  477 HIS cc_start: 0.5551 (m-70) cc_final: 0.4825 (m-70)
REVERT: A  155 ILE cc_start: 0.8190 (mm) cc_final: 0.7971 (mt)
REVERT: A  396 GLN cc_start: 0.8521 (tp-100) cc_final: 0.7810 (tt0)
REVERT: A  495 LEU cc_start: 0.7756 (mt) cc_final: 0.7521 (mt)
REVERT: A  510 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6662 (pt)
  outliers start: 34
  outliers final: 23
  residues processed: 154
  average time/residue: 0.0849
  time to fit residues: 17.5316
Evaluate side-chains
  157 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  358 PHE
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  456 TRP
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  462 VAL
Chi-restraints excluded: chain B residue  516 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  516 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9990
   chunk 75 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 78 optimal weight:    8.9990
   chunk 79 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
B 286 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.202492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.173834 restraints weight = 7691.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.172375 restraints weight = 10239.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.172779 restraints weight = 10820.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.171840 restraints weight = 9190.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.171987 restraints weight = 9340.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6899
moved from start:          0.3903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7056  Z= 0.165
  Angle     :  0.656   8.745   9646  Z= 0.316
  Chirality :  0.041   0.163   1204
  Planarity :  0.004   0.038   1118
  Dihedral  : 12.979 178.597   1647
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 16.43 %
    Favored  : 78.67 %
  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 are not related in a simple way.
  whole:  1.09 (0.30), residues: 858
  helix:  1.65 (0.20), residues: 642
  sheet:  None (None), residues: 0
  loop : -2.22 (0.47), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 156 
 TYR   0.008   0.001   TYR B 260 
 PHE   0.009   0.001   PHE A 494 
 TRP   0.010   0.001   TRP A  97 
 HIS   0.004   0.001   HIS B 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 7056)
  covalent geometry    : angle       0.65640 ( 9646)
  hydrogen bonds       : bond        0.05566 (  449)
  hydrogen bonds       : angle       3.97772 ( 1347)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 0.236 
Fit side-chains
TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it.
REVERT: B   82 LEU cc_start: 0.4729 (OUTLIER) cc_final: 0.4399 (tp)
REVERT: B  279 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7794 (mp)
REVERT: B  358 PHE cc_start: 0.6844 (OUTLIER) cc_final: 0.5662 (p90)
REVERT: B  477 HIS cc_start: 0.5423 (m-70) cc_final: 0.4672 (m-70)
REVERT: A  155 ILE cc_start: 0.8191 (mm) cc_final: 0.7977 (mt)
REVERT: A  364 LEU cc_start: 0.6955 (pp) cc_final: 0.6754 (tp)
REVERT: A  396 GLN cc_start: 0.8540 (tp-100) cc_final: 0.7807 (tt0)
REVERT: A  495 LEU cc_start: 0.7743 (mt) cc_final: 0.7500 (mt)
REVERT: A  510 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6725 (pt)
  outliers start: 34
  outliers final: 27
  residues processed: 154
  average time/residue: 0.0829
  time to fit residues: 17.3145
Evaluate side-chains
  160 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  358 PHE
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  462 VAL
Chi-restraints excluded: chain B residue  506 LEU
Chi-restraints excluded: chain B residue  516 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  516 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0570
   chunk 73 optimal weight:    3.9990
   overall best weight:    1.1502

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

Flipped N/Q/H residues before XYZ refinement:
B 286 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.199757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.164470 restraints weight = 7578.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.161706 restraints weight = 11351.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.163209 restraints weight = 11890.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.162349 restraints weight = 8996.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.163477 restraints weight = 9765.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.4052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7056  Z= 0.139
  Angle     :  0.618   6.300   9646  Z= 0.298
  Chirality :  0.039   0.146   1204
  Planarity :  0.004   0.035   1118
  Dihedral  : 12.578 175.511   1647
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 17.58 %
    Favored  : 78.24 %
  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 are not related in a simple way.
  whole:  1.26 (0.30), residues: 858
  helix:  1.76 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -2.15 (0.47), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 156 
 TYR   0.008   0.001   TYR B 260 
 PHE   0.017   0.001   PHE A 494 
 TRP   0.011   0.001   TRP A  97 
 HIS   0.004   0.001   HIS B 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7056)
  covalent geometry    : angle       0.61766 ( 9646)
  hydrogen bonds       : bond        0.05042 (  449)
  hydrogen bonds       : angle       3.88052 ( 1347)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 133
  time to evaluate  : 0.264 
Fit side-chains
TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it.
REVERT: B   82 LEU cc_start: 0.5036 (OUTLIER) cc_final: 0.4717 (tp)
REVERT: B  223 TYR cc_start: 0.7327 (t80) cc_final: 0.7119 (t80)
REVERT: B  279 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7757 (mp)
REVERT: B  358 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.5662 (p90)
REVERT: A  155 ILE cc_start: 0.8135 (mm) cc_final: 0.7899 (mt)
REVERT: A  364 LEU cc_start: 0.6940 (pp) cc_final: 0.6730 (tp)
REVERT: A  396 GLN cc_start: 0.8532 (tp-100) cc_final: 0.7806 (tt0)
REVERT: A  510 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6641 (pt)
  outliers start: 29
  outliers final: 24
  residues processed: 150
  average time/residue: 0.0825
  time to fit residues: 16.7810
Evaluate side-chains
  158 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  358 PHE
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  462 VAL
Chi-restraints excluded: chain B residue  516 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  516 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 81 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0770
   chunk 0 optimal weight:   10.0000
   chunk 75 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0470
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.5036

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

Flipped N/Q/H residues before XYZ refinement:
A 481 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.207882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.181740 restraints weight = 7611.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.176645 restraints weight = 10764.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.174775 restraints weight = 12061.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.174095 restraints weight = 11390.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.174496 restraints weight = 10081.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
moved from start:          0.4223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7056  Z= 0.115
  Angle     :  0.594   7.904   9646  Z= 0.285
  Chirality :  0.038   0.166   1204
  Planarity :  0.004   0.034   1118
  Dihedral  : 12.208 174.880   1647
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 18.59 %
    Favored  : 77.38 %
  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 are not related in a simple way.
  whole:  1.57 (0.30), residues: 858
  helix:  1.98 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -2.03 (0.49), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 156 
 TYR   0.007   0.001   TYR A 260 
 PHE   0.017   0.001   PHE A 494 
 TRP   0.013   0.001   TRP A  97 
 HIS   0.003   0.001   HIS B 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 7056)
  covalent geometry    : angle       0.59362 ( 9646)
  hydrogen bonds       : bond        0.04213 (  449)
  hydrogen bonds       : angle       3.72128 ( 1347)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.241 
Fit side-chains
TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it.
REVERT: B   82 LEU cc_start: 0.4913 (OUTLIER) cc_final: 0.4589 (tp)
REVERT: B  358 PHE cc_start: 0.6721 (OUTLIER) cc_final: 0.5600 (p90)
REVERT: A  291 MET cc_start: 0.5000 (mmp) cc_final: 0.4574 (mtt)
REVERT: A  396 GLN cc_start: 0.8468 (tp-100) cc_final: 0.7770 (tt0)
REVERT: A  510 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6611 (pt)
  outliers start: 28
  outliers final: 21
  residues processed: 151
  average time/residue: 0.0826
  time to fit residues: 16.8204
Evaluate side-chains
  153 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  358 PHE
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  462 VAL
Chi-restraints excluded: chain B residue  516 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  516 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   chunk 60 optimal weight:    0.0040
   chunk 21 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
A 481 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.203335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.170080 restraints weight = 7618.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.166974 restraints weight = 10098.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.168599 restraints weight = 11040.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.167831 restraints weight = 8536.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.167940 restraints weight = 8319.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6867
moved from start:          0.4338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7056  Z= 0.117
  Angle     :  0.604   7.986   9646  Z= 0.291
  Chirality :  0.039   0.170   1204
  Planarity :  0.004   0.035   1118
  Dihedral  : 12.016 175.177   1647
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 18.59 %
    Favored  : 77.38 %
  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 are not related in a simple way.
  whole:  1.63 (0.30), residues: 858
  helix:  2.01 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.98 (0.49), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 475 
 TYR   0.016   0.001   TYR B 223 
 PHE   0.015   0.001   PHE A 494 
 TRP   0.011   0.001   TRP A  97 
 HIS   0.003   0.001   HIS B 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 7056)
  covalent geometry    : angle       0.60386 ( 9646)
  hydrogen bonds       : bond        0.04194 (  449)
  hydrogen bonds       : angle       3.70718 ( 1347)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 0.244 
Fit side-chains
TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it.
REVERT: B   82 LEU cc_start: 0.5058 (OUTLIER) cc_final: 0.4738 (tp)
REVERT: B  358 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.5649 (p90)
REVERT: A  291 MET cc_start: 0.5133 (mmp) cc_final: 0.4759 (mtt)
REVERT: A  364 LEU cc_start: 0.6888 (pp) cc_final: 0.6664 (tp)
REVERT: A  396 GLN cc_start: 0.8435 (tp-100) cc_final: 0.7718 (tt0)
REVERT: A  510 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6596 (pt)
  outliers start: 28
  outliers final: 20
  residues processed: 154
  average time/residue: 0.0765
  time to fit residues: 16.0025
Evaluate side-chains
  158 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  358 PHE
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  462 VAL
Chi-restraints excluded: chain B residue  516 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  516 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 84 optimal weight:    0.9990
   chunk 67 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 77 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 286 ASN
A 481 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.205338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.178914 restraints weight = 7526.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.175460 restraints weight = 11950.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.174316 restraints weight = 11838.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.172671 restraints weight = 12197.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.173856 restraints weight = 10511.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7056  Z= 0.129
  Angle     :  0.628   8.027   9646  Z= 0.304
  Chirality :  0.040   0.310   1204
  Planarity :  0.004   0.035   1118
  Dihedral  : 11.950 175.475   1647
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 19.31 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.30), residues: 858
  helix:  1.91 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -2.00 (0.49), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 475 
 TYR   0.014   0.001   TYR B 223 
 PHE   0.016   0.001   PHE A 494 
 TRP   0.009   0.001   TRP B 392 
 HIS   0.003   0.001   HIS B 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7056)
  covalent geometry    : angle       0.62819 ( 9646)
  hydrogen bonds       : bond        0.04441 (  449)
  hydrogen bonds       : angle       3.74241 ( 1347)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.274 
Fit side-chains
TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it.
REVERT: B   82 LEU cc_start: 0.4935 (OUTLIER) cc_final: 0.4589 (tp)
REVERT: B  358 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.5669 (p90)
REVERT: A  291 MET cc_start: 0.5084 (mmp) cc_final: 0.4700 (mtt)
REVERT: A  396 GLN cc_start: 0.8433 (tp-100) cc_final: 0.7758 (tt0)
REVERT: A  510 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6620 (pt)
  outliers start: 25
  outliers final: 21
  residues processed: 146
  average time/residue: 0.0835
  time to fit residues: 16.5868
Evaluate side-chains
  154 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  358 PHE
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  462 VAL
Chi-restraints excluded: chain B residue  516 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  516 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0670
   chunk 66 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A 481 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.204572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.171896 restraints weight = 7550.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.168557 restraints weight = 12234.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.170822 restraints weight = 11576.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.170142 restraints weight = 8781.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.170277 restraints weight = 8296.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6881
moved from start:          0.4463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7056  Z= 0.118
  Angle     :  0.610   8.252   9646  Z= 0.294
  Chirality :  0.039   0.256   1204
  Planarity :  0.004   0.034   1118
  Dihedral  : 11.805 176.125   1647
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 19.45 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.30), residues: 858
  helix:  2.00 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -2.01 (0.48), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 475 
 TYR   0.013   0.001   TYR B 223 
 PHE   0.015   0.001   PHE A 494 
 TRP   0.011   0.001   TRP A  97 
 HIS   0.002   0.001   HIS B 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 7056)
  covalent geometry    : angle       0.60996 ( 9646)
  hydrogen bonds       : bond        0.04125 (  449)
  hydrogen bonds       : angle       3.68856 ( 1347)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1167.41 seconds
wall clock time: 20 minutes 53.35 seconds (1253.35 seconds total)