Starting phenix.real_space_refine
on Tue Mar  3 17:15:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7en0_31197/03_2026/7en0_31197.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7en0_31197/03_2026/7en0_31197.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7en0_31197/03_2026/7en0_31197.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7en0_31197/03_2026/7en0_31197.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7en0_31197/03_2026/7en0_31197.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7en0_31197/03_2026/7en0_31197.cif"
  }
  resolution = 2.97
  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=   1.000
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       3      5.49       5
     S      48      5.16       5
     C    4878      2.51       5
     N    1137      2.21       5
     O    1173      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7239
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2350
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 313, 2339
          Classifications: {'peptide': 313}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 15, 'TRANS': 297}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 145
          Unresolved non-hydrogen dihedrals: 111
          Planarities with less than four sites: {'TRP:plan': 2, 'ARG:plan': 8, 'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3}
          Unresolved non-hydrogen planarities: 88
      Conformer: "B"
        Number of residues, atoms: 313, 2339
          Classifications: {'peptide': 313}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 15, 'TRANS': 297}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 145
          Unresolved non-hydrogen dihedrals: 111
          Planarities with less than four sites: {'TRP:plan': 2, 'ARG:plan': 8, 'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3}
          Unresolved non-hydrogen planarities: 88
          bond proxies already assigned to first conformer: 2399
    Chain: "A"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 63
          Unusual residues: {'PLC': 1, 'SPH': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, C
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  AARG A 357 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 357 " occ=0.50
    residue:
      pdb=" N  AARG B 357 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG B 357 " occ=0.50
    residue:
      pdb=" N  AARG C 357 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG C 357 " occ=0.50
  Time building chain proxies: 1.74, per 1000 atoms: 0.24
  Number of scatterers: 7239
  At special positions: 0
  Unit cell: (106.845, 105.797, 62.85, 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      48     16.00
     P       3     15.00
     O    1173      8.00
     N    1137      7.00
     C    4878      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: 0.80
  Conformation dependent library (CDL) restraints added in 436.6 milliseconds
  

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1782

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 0 sheets defined
      81.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 193 through 197
    Processing helix  chain 'A' and resid 198 through 200
      No H-bonds generated for 'chain 'A' and resid 198 through 200'
    Processing helix  chain 'A' and resid 201 through 221
      removed outlier: 3.986A  pdb=" N   CYS A 205 " --> pdb=" O   CYS A 201 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   GLN A 211 " --> pdb=" O   GLY A 207 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA A 212 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE A 213 " --> pdb=" O   GLY A 209 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU A 214 " --> pdb=" O   SER A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 259
      removed outlier: 4.409A  pdb=" N   ASN A 234 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU A 235 " --> pdb=" O   PRO A 231 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   TYR A 252 " --> pdb=" O   THR A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 268
      removed outlier: 4.109A  pdb=" N   ILE A 263 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ARG A 264 " --> pdb=" O   PHE A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 276
    Processing helix  chain 'A' and resid 277 through 289
      removed outlier: 4.227A  pdb=" N   ALA A 283 " --> pdb=" O   PRO A 279 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY A 289 " --> pdb=" O   PHE A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 328
      removed outlier: 3.544A  pdb=" N   SER A 310 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      Proline residue:  A 313  - end of helix
      removed outlier: 3.559A  pdb=" N   LEU A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU A 326 " --> pdb=" O   TYR A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 336
    Processing helix  chain 'A' and resid 338 through 344
      removed outlier: 3.710A  pdb=" N   HIS A 342 " --> pdb=" O   PRO A 339 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A 343 " --> pdb=" O   SER A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 359
      removed outlier: 3.731A  pdb=" N   PHE A 349 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 382
      removed outlier: 3.890A  pdb=" N   HIS A 374 " --> pdb=" O   ILE A 370 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL A 377 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 403
      removed outlier: 3.553A  pdb=" N   SER A 401 " --> pdb=" O   PRO A 398 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   MET A 402 " --> pdb=" O   VAL A 399 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   PHE A 403 " --> pdb=" O   TYR A 400 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 398 through 403'
    Processing helix  chain 'A' and resid 404 through 418
    Processing helix  chain 'A' and resid 423 through 443
      removed outlier: 3.708A  pdb=" N   VAL A 441 " --> pdb=" O   MET A 437 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   ARG A 442 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 458
    Processing helix  chain 'A' and resid 459 through 476
      removed outlier: 3.658A  pdb=" N   THR A 469 " --> pdb=" O   ALA A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 507
      removed outlier: 3.561A  pdb=" N   MET A 495 " --> pdb=" O   MET A 491 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU A 505 " --> pdb=" O   VAL A 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 197
    Processing helix  chain 'B' and resid 198 through 200
      No H-bonds generated for 'chain 'B' and resid 198 through 200'
    Processing helix  chain 'B' and resid 201 through 221
      removed outlier: 3.985A  pdb=" N   CYS B 205 " --> pdb=" O   CYS B 201 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   GLN B 211 " --> pdb=" O   GLY B 207 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA B 212 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ILE B 213 " --> pdb=" O   GLY B 209 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU B 214 " --> pdb=" O   SER B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 259
      removed outlier: 4.409A  pdb=" N   ASN B 234 " --> pdb=" O   THR B 230 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU B 235 " --> pdb=" O   PRO B 231 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   TYR B 252 " --> pdb=" O   THR B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 268
      removed outlier: 4.109A  pdb=" N   ILE B 263 " --> pdb=" O   TYR B 259 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ARG B 264 " --> pdb=" O   PHE B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 276
    Processing helix  chain 'B' and resid 277 through 289
      removed outlier: 4.227A  pdb=" N   ALA B 283 " --> pdb=" O   PRO B 279 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY B 289 " --> pdb=" O   PHE B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 328
      removed outlier: 3.545A  pdb=" N   SER B 310 " --> pdb=" O   VAL B 306 " (cutoff:3.500A)
      Proline residue:  B 313  - end of helix
      removed outlier: 3.560A  pdb=" N   LEU B 317 " --> pdb=" O   PRO B 313 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU B 326 " --> pdb=" O   TYR B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 336
    Processing helix  chain 'B' and resid 338 through 344
      removed outlier: 3.709A  pdb=" N   HIS B 342 " --> pdb=" O   PRO B 339 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU B 343 " --> pdb=" O   SER B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 359
      removed outlier: 3.731A  pdb=" N   PHE B 349 " --> pdb=" O   VAL B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 382
      removed outlier: 3.890A  pdb=" N   HIS B 374 " --> pdb=" O   ILE B 370 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL B 377 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 398 through 403
      removed outlier: 3.553A  pdb=" N   SER B 401 " --> pdb=" O   PRO B 398 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   MET B 402 " --> pdb=" O   VAL B 399 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   PHE B 403 " --> pdb=" O   TYR B 400 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 398 through 403'
    Processing helix  chain 'B' and resid 404 through 418
    Processing helix  chain 'B' and resid 423 through 443
      removed outlier: 3.708A  pdb=" N   VAL B 441 " --> pdb=" O   MET B 437 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ARG B 442 " --> pdb=" O   SER B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 458
    Processing helix  chain 'B' and resid 459 through 476
      removed outlier: 3.658A  pdb=" N   THR B 469 " --> pdb=" O   ALA B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 507
      removed outlier: 3.561A  pdb=" N   MET B 495 " --> pdb=" O   MET B 491 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU B 505 " --> pdb=" O   VAL B 501 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 193 through 197
    Processing helix  chain 'C' and resid 198 through 200
      No H-bonds generated for 'chain 'C' and resid 198 through 200'
    Processing helix  chain 'C' and resid 201 through 221
      removed outlier: 3.986A  pdb=" N   CYS C 205 " --> pdb=" O   CYS C 201 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   GLN C 211 " --> pdb=" O   GLY C 207 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ALA C 212 " --> pdb=" O   LEU C 208 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE C 213 " --> pdb=" O   GLY C 209 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU C 214 " --> pdb=" O   SER C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 259
      removed outlier: 4.409A  pdb=" N   ASN C 234 " --> pdb=" O   THR C 230 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU C 235 " --> pdb=" O   PRO C 231 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   TYR C 252 " --> pdb=" O   THR C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 268
      removed outlier: 4.110A  pdb=" N   ILE C 263 " --> pdb=" O   TYR C 259 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ARG C 264 " --> pdb=" O   PHE C 260 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 273 through 276
    Processing helix  chain 'C' and resid 277 through 289
      removed outlier: 4.226A  pdb=" N   ALA C 283 " --> pdb=" O   PRO C 279 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY C 289 " --> pdb=" O   PHE C 285 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 304 through 328
      removed outlier: 3.545A  pdb=" N   SER C 310 " --> pdb=" O   VAL C 306 " (cutoff:3.500A)
      Proline residue:  C 313  - end of helix
      removed outlier: 3.559A  pdb=" N   LEU C 317 " --> pdb=" O   PRO C 313 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU C 326 " --> pdb=" O   TYR C 322 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 336
    Processing helix  chain 'C' and resid 338 through 344
      removed outlier: 3.710A  pdb=" N   HIS C 342 " --> pdb=" O   PRO C 339 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU C 343 " --> pdb=" O   SER C 340 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 345 through 359
      removed outlier: 3.731A  pdb=" N   PHE C 349 " --> pdb=" O   VAL C 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 360 through 382
      removed outlier: 3.889A  pdb=" N   HIS C 374 " --> pdb=" O   ILE C 370 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL C 377 " --> pdb=" O   ALA C 373 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 398 through 403
      removed outlier: 3.553A  pdb=" N   SER C 401 " --> pdb=" O   PRO C 398 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   MET C 402 " --> pdb=" O   VAL C 399 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   PHE C 403 " --> pdb=" O   TYR C 400 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 398 through 403'
    Processing helix  chain 'C' and resid 404 through 418
    Processing helix  chain 'C' and resid 423 through 443
      removed outlier: 3.708A  pdb=" N   VAL C 441 " --> pdb=" O   MET C 437 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   ARG C 442 " --> pdb=" O   SER C 438 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 453 through 458
    Processing helix  chain 'C' and resid 459 through 476
      removed outlier: 3.658A  pdb=" N   THR C 469 " --> pdb=" O   ALA C 465 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 479 through 507
      removed outlier: 3.561A  pdb=" N   MET C 495 " --> pdb=" O   MET C 491 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU C 505 " --> pdb=" O   VAL C 501 " (cutoff:3.500A)

    483 hydrogen bonds defined for protein.
    1362 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: 1.10

  Time building geometry restraints manager: 0.98 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: 1008
        1.31 -     1.43: 2194
        1.43 -     1.56: 4166
        1.56 -     1.68: 6
        1.68 -     1.81: 78
  Bond restraints: 7452
  Sorted by residual:
  bond pdb=" C4  SPH A 602 "
       pdb=" C5  SPH A 602 "
    ideal  model  delta    sigma   weight residual
    1.334  1.473 -0.139 2.00e-02 2.50e+03 4.80e+01
  bond pdb=" C4  SPH C 602 "
       pdb=" C5  SPH C 602 "
    ideal  model  delta    sigma   weight residual
    1.334  1.472 -0.138 2.00e-02 2.50e+03 4.79e+01
  bond pdb=" C4  SPH B 602 "
       pdb=" C5  SPH B 602 "
    ideal  model  delta    sigma   weight residual
    1.334  1.472 -0.138 2.00e-02 2.50e+03 4.79e+01
  bond pdb=" CB  PLC B 601 "
       pdb=" O3  PLC B 601 "
    ideal  model  delta    sigma   weight residual
    1.327  1.398 -0.071 2.00e-02 2.50e+03 1.25e+01
  bond pdb=" CB  PLC C 601 "
       pdb=" O3  PLC C 601 "
    ideal  model  delta    sigma   weight residual
    1.327  1.397 -0.070 2.00e-02 2.50e+03 1.23e+01
  ... (remaining 7447 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.17: 9932
        3.17 -     6.33: 208
        6.33 -     9.50: 27
        9.50 -    12.66: 3
       12.66 -    15.83: 3
  Bond angle restraints: 10173
  Sorted by residual:
  angle pdb=" O3P PLC B 601 "
        pdb=" P   PLC B 601 "
        pdb=" O4P PLC B 601 "
      ideal   model   delta    sigma   weight residual
      93.62  109.45  -15.83 3.00e+00 1.11e-01 2.78e+01
  angle pdb=" O3P PLC A 601 "
        pdb=" P   PLC A 601 "
        pdb=" O4P PLC A 601 "
      ideal   model   delta    sigma   weight residual
      93.62  109.44  -15.82 3.00e+00 1.11e-01 2.78e+01
  angle pdb=" O3P PLC C 601 "
        pdb=" P   PLC C 601 "
        pdb=" O4P PLC C 601 "
      ideal   model   delta    sigma   weight residual
      93.62  109.43  -15.81 3.00e+00 1.11e-01 2.78e+01
  angle pdb=" N   LEU B 504 "
        pdb=" CA  LEU B 504 "
        pdb=" C   LEU B 504 "
      ideal   model   delta    sigma   weight residual
     113.20  106.98    6.22 1.21e+00 6.83e-01 2.64e+01
  angle pdb=" N   LEU C 504 "
        pdb=" CA  LEU C 504 "
        pdb=" C   LEU C 504 "
      ideal   model   delta    sigma   weight residual
     113.20  107.01    6.19 1.21e+00 6.83e-01 2.62e+01
  ... (remaining 10168 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.40: 4059
       28.40 -    56.80: 222
       56.80 -    85.21: 6
       85.21 -   113.61: 0
      113.61 -   142.01: 9
  Dihedral angle restraints: 4296
    sinusoidal: 1545
      harmonic: 2751
  Sorted by residual:
  dihedral pdb=" C1B PLC A 601 "
           pdb=" CB  PLC A 601 "
           pdb=" O3  PLC A 601 "
           pdb=" C3  PLC A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     181.23   39.22  142.01     1      3.00e+01 1.11e-03 1.91e+01
  dihedral pdb=" C1B PLC B 601 "
           pdb=" CB  PLC B 601 "
           pdb=" O3  PLC B 601 "
           pdb=" C3  PLC B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     181.23   39.22  142.01     1      3.00e+01 1.11e-03 1.91e+01
  dihedral pdb=" C1B PLC C 601 "
           pdb=" CB  PLC C 601 "
           pdb=" O3  PLC C 601 "
           pdb=" C3  PLC C 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     181.23   39.26  141.97     1      3.00e+01 1.11e-03 1.91e+01
  ... (remaining 4293 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 882
       0.049 -    0.097: 230
       0.097 -    0.146: 43
       0.146 -    0.194: 15
       0.194 -    0.243: 21
  Chirality restraints: 1191
  Sorted by residual:
  chirality pdb=" C3  SPH C 602 "
            pdb=" C2  SPH C 602 "
            pdb=" C4  SPH C 602 "
            pdb=" O3  SPH C 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.18    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" C3  SPH A 602 "
            pdb=" C2  SPH A 602 "
            pdb=" C4  SPH A 602 "
            pdb=" O3  SPH A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.18    0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" C3  SPH B 602 "
            pdb=" C2  SPH B 602 "
            pdb=" C4  SPH B 602 "
            pdb=" O3  SPH B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.18    0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 1188 not shown)

  Planarity restraints: 1218
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3  SPH B 602 "    0.043 2.00e-02 2.50e+03   4.38e-02 1.92e+01
        pdb=" C4  SPH B 602 "   -0.040 2.00e-02 2.50e+03
        pdb=" C5  SPH B 602 "   -0.047 2.00e-02 2.50e+03
        pdb=" C6  SPH B 602 "    0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3  SPH C 602 "   -0.043 2.00e-02 2.50e+03   4.37e-02 1.91e+01
        pdb=" C4  SPH C 602 "    0.040 2.00e-02 2.50e+03
        pdb=" C5  SPH C 602 "    0.047 2.00e-02 2.50e+03
        pdb=" C6  SPH C 602 "   -0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3  SPH A 602 "    0.043 2.00e-02 2.50e+03   4.37e-02 1.91e+01
        pdb=" C4  SPH A 602 "   -0.040 2.00e-02 2.50e+03
        pdb=" C5  SPH A 602 "   -0.047 2.00e-02 2.50e+03
        pdb=" C6  SPH A 602 "    0.044 2.00e-02 2.50e+03
  ... (remaining 1215 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2269
        2.82 -     3.34: 6826
        3.34 -     3.86: 12171
        3.86 -     4.38: 14508
        4.38 -     4.90: 24431
  Nonbonded interactions: 60205
  Sorted by model distance:
  nonbonded pdb=" O   THR B 459 "
            pdb=" OG1 THR B 463 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   THR A 459 "
            pdb=" OG1 THR A 463 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   THR C 459 "
            pdb=" OG1 THR C 463 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   SER C 340 "
            pdb=" OG  SER C 340 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" O   SER B 340 "
            pdb=" OG  SER B 340 "
     model   vdw
     2.325 3.040
  ... (remaining 60200 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.38 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             0.440
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.290
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.139   7452  Z= 0.391
  Angle     :  1.079  15.827  10173  Z= 0.600
  Chirality :  0.054   0.243   1191
  Planarity :  0.005   0.044   1218
  Dihedral  : 17.393 142.011   2514
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  4.21 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 15.72 %
    Favored  : 79.48 %
  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: -3.26 (0.25), residues: 936
  helix: -2.04 (0.17), residues: 681
  sheet:  None (None), residues: 0
  loop : -1.92 (0.42), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 225 
 TYR   0.007   0.001   TYR C 400 
 PHE   0.017   0.001   PHE A 421 
 TRP   0.008   0.001   TRP B 215 
 HIS   0.005   0.001   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00710 ( 7452)
  covalent geometry    : angle       1.07886 (10173)
  hydrogen bonds       : bond        0.17744 (  483)
  hydrogen bonds       : angle       6.69506 ( 1362)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 126
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7285 (mt)
REVERT: A  332 ARG cc_start: 0.6296 (ttp-110) cc_final: 0.5481 (ttt90)
REVERT: A  482 ARG cc_start: 0.7212 (ttm170) cc_final: 0.6940 (mtm-85)
REVERT: A  491 MET cc_start: 0.7328 (ttm) cc_final: 0.7032 (ttm)
REVERT: A  505 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6175 (mp)
REVERT: B  263 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7086 (mt)
REVERT: B  264 ARG cc_start: 0.6791 (mtm-85) cc_final: 0.6534 (mtm180)
REVERT: B  327 SER cc_start: 0.7766 (OUTLIER) cc_final: 0.7538 (p)
REVERT: B  332 ARG cc_start: 0.6177 (ttp-110) cc_final: 0.5386 (ttt90)
REVERT: B  491 MET cc_start: 0.7502 (ttm) cc_final: 0.7290 (ttm)
REVERT: B  505 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5963 (mp)
REVERT: C  264 ARG cc_start: 0.6824 (mtm-85) cc_final: 0.6416 (ttp-110)
REVERT: C  267 PHE cc_start: 0.7844 (t80) cc_final: 0.7498 (t80)
REVERT: C  272 ARG cc_start: 0.7006 (mtt180) cc_final: 0.6666 (mtt180)
REVERT: C  331 ARG cc_start: 0.7073 (mtm-85) cc_final: 0.5703 (mmm160)
REVERT: C  332 ARG cc_start: 0.6126 (ttp-110) cc_final: 0.5264 (ttt90)
REVERT: C  455 TRP cc_start: 0.6427 (t-100) cc_final: 0.6210 (t-100)
REVERT: C  482 ARG cc_start: 0.7385 (ttm170) cc_final: 0.7153 (ttm-80)
REVERT: C  505 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.6048 (mp)
  outliers start: 30
  outliers final: 7
  residues processed: 148
  average time/residue: 0.5214
  time to fit residues: 81.4852
Evaluate side-chains
  118 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  263 ILE
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  442 ARG
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain C residue  327 SER
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  505 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:   20.0000
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 303 HIS
A 348 ASN
A 374 HIS
B 348 ASN
B 374 HIS
C 374 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.155697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.110601 restraints weight = 24872.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 4.94
r_work: 0.2853 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2773
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2773 r_free = 0.2773    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2735 r_free = 0.2735    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2735
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.1581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7452  Z= 0.131
  Angle     :  0.595   9.652  10173  Z= 0.293
  Chirality :  0.038   0.119   1191
  Planarity :  0.005   0.029   1218
  Dihedral  : 16.611 145.540   1195
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 21.69 %
    Favored  : 75.98 %
  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: -1.17 (0.27), residues: 936
  helix: -0.46 (0.19), residues: 681
  sheet:  None (None), residues: 0
  loop : -1.27 (0.42), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 264 
 TYR   0.019   0.002   TYR B 259 
 PHE   0.021   0.001   PHE B 260 
 TRP   0.013   0.001   TRP B 455 
 HIS   0.004   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 7452)
  covalent geometry    : angle       0.59533 (10173)
  hydrogen bonds       : bond        0.03931 (  483)
  hydrogen bonds       : angle       4.16752 ( 1362)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 ARG cc_start: 0.6485 (mtm-85) cc_final: 0.6185 (ttp-110)
REVERT: A  332 ARG cc_start: 0.6125 (ttp-110) cc_final: 0.5232 (ttt90)
REVERT: C  264 ARG cc_start: 0.6515 (mtm-85) cc_final: 0.6274 (mtm180)
REVERT: C  272 ARG cc_start: 0.7631 (mtt180) cc_final: 0.7360 (mtt180)
REVERT: C  501 VAL cc_start: 0.7893 (m) cc_final: 0.7654 (t)
REVERT: C  505 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6061 (mp)
  outliers start: 13
  outliers final: 3
  residues processed: 104
  average time/residue: 0.6458
  time to fit residues: 70.3328
Evaluate side-chains
  95 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain C residue  442 ARG
Chi-restraints excluded: chain C residue  505 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0020
   chunk 88 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.7190

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.153652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.108960 restraints weight = 22575.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 4.71
r_work: 0.2842 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2727
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2727 r_free = 0.2727    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2727 r_free = 0.2727    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2727
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7452  Z= 0.124
  Angle     :  0.569  10.380  10173  Z= 0.277
  Chirality :  0.037   0.121   1191
  Planarity :  0.004   0.030   1218
  Dihedral  : 15.560 149.893   1175
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 23.87 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.05 (0.28), residues: 936
  helix:  0.26 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop : -0.53 (0.45), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 331 
 TYR   0.016   0.001   TYR C 259 
 PHE   0.028   0.001   PHE C 267 
 TRP   0.021   0.001   TRP B 455 
 HIS   0.002   0.001   HIS B 342 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7452)
  covalent geometry    : angle       0.56900 (10173)
  hydrogen bonds       : bond        0.03815 (  483)
  hydrogen bonds       : angle       3.92009 ( 1362)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ARG cc_start: 0.7469 (mpp80) cc_final: 0.6072 (mmm160)
REVERT: A  332 ARG cc_start: 0.6153 (ttp-110) cc_final: 0.5282 (ttt90)
REVERT: A  505 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6203 (mp)
REVERT: B  224 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.6445 (mmm)
REVERT: B  314 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8324 (tt)
REVERT: B  442 ARG cc_start: 0.5978 (OUTLIER) cc_final: 0.4977 (mpt180)
REVERT: C  272 ARG cc_start: 0.7683 (mtt180) cc_final: 0.7382 (mtt180)
REVERT: C  501 VAL cc_start: 0.7782 (m) cc_final: 0.7576 (t)
REVERT: C  505 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5961 (mp)
  outliers start: 11
  outliers final: 1
  residues processed: 104
  average time/residue: 0.5997
  time to fit residues: 65.5530
Evaluate side-chains
  96 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain B residue  224 MET
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  442 ARG
Chi-restraints excluded: chain C residue  442 ARG
Chi-restraints excluded: chain C residue  505 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 67 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 88 optimal weight:    0.8980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 348 ASN
B 348 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.152588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.106289 restraints weight = 27917.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 5.06
r_work: 0.2806 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2677
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2677 r_free = 0.2677    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2677 r_free = 0.2677    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2677
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7452  Z= 0.135
  Angle     :  0.576   9.489  10173  Z= 0.278
  Chirality :  0.038   0.126   1191
  Planarity :  0.004   0.030   1218
  Dihedral  : 15.007 151.793   1175
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 25.62 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.41 (0.29), residues: 936
  helix:  0.61 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop : -0.39 (0.45), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 264 
 TYR   0.021   0.001   TYR A 259 
 PHE   0.022   0.001   PHE C 267 
 TRP   0.025   0.001   TRP B 455 
 HIS   0.002   0.001   HIS B 342 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7452)
  covalent geometry    : angle       0.57581 (10173)
  hydrogen bonds       : bond        0.03822 (  483)
  hydrogen bonds       : angle       3.85498 ( 1362)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ARG cc_start: 0.7512 (mpp80) cc_final: 0.6245 (mmm160)
REVERT: A  332 ARG cc_start: 0.6363 (ttp-110) cc_final: 0.5510 (ttt90)
REVERT: A  505 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6289 (mp)
REVERT: B  314 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8418 (tt)
REVERT: B  331 ARG cc_start: 0.7437 (mpp80) cc_final: 0.6085 (mmm160)
REVERT: C  264 ARG cc_start: 0.6575 (ttp-110) cc_final: 0.6275 (ttp-110)
REVERT: C  272 ARG cc_start: 0.7792 (mtt180) cc_final: 0.7454 (mtt180)
REVERT: C  505 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5935 (mp)
  outliers start: 10
  outliers final: 2
  residues processed: 101
  average time/residue: 0.5944
  time to fit residues: 63.1372
Evaluate side-chains
  97 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain C residue  442 ARG
Chi-restraints excluded: chain C residue  505 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 91 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 348 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.152713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.107585 restraints weight = 22956.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 4.54
r_work: 0.2832 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2728
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2728 r_free = 0.2728    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2728 r_free = 0.2728    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2728
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7452  Z= 0.128
  Angle     :  0.558   8.845  10173  Z= 0.271
  Chirality :  0.038   0.124   1191
  Planarity :  0.004   0.029   1218
  Dihedral  : 14.759 151.263   1175
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 26.35 %
    Favored  : 71.76 %
  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:  0.78 (0.29), residues: 936
  helix:  0.88 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop : -0.26 (0.45), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 264 
 TYR   0.018   0.001   TYR B 259 
 PHE   0.022   0.001   PHE B 479 
 TRP   0.025   0.001   TRP B 455 
 HIS   0.002   0.001   HIS B 342 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7452)
  covalent geometry    : angle       0.55824 (10173)
  hydrogen bonds       : bond        0.03731 (  483)
  hydrogen bonds       : angle       3.79233 ( 1362)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  331 ARG cc_start: 0.7459 (mpp80) cc_final: 0.6189 (mmm160)
REVERT: A  332 ARG cc_start: 0.6339 (ttp-110) cc_final: 0.5463 (ttt90)
REVERT: A  421 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.7612 (m-80)
REVERT: A  505 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6104 (mp)
REVERT: B  331 ARG cc_start: 0.7398 (mpp80) cc_final: 0.6101 (mmm160)
REVERT: C  264 ARG cc_start: 0.6472 (ttp-110) cc_final: 0.6149 (ttp-110)
REVERT: C  272 ARG cc_start: 0.7649 (mtt180) cc_final: 0.7304 (mtt180)
  outliers start: 10
  outliers final: 1
  residues processed: 101
  average time/residue: 0.6267
  time to fit residues: 66.3971
Evaluate side-chains
  96 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain B residue  421 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 76 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   chunk 65 optimal weight:    8.9990
   chunk 55 optimal weight:    9.9990
   chunk 45 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
A 234 ASN
** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 348 ASN
C 234 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.149049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.104098 restraints weight = 22745.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 4.31
r_work: 0.2778 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2770
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2770
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7452  Z= 0.187
  Angle     :  0.608   8.181  10173  Z= 0.296
  Chirality :  0.040   0.131   1191
  Planarity :  0.004   0.030   1218
  Dihedral  : 14.699 147.576   1173
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 27.22 %
    Favored  : 71.18 %
  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:  0.74 (0.29), residues: 936
  helix:  0.84 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop : -0.23 (0.45), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 264 
 TYR   0.016   0.001   TYR A 259 
 PHE   0.020   0.002   PHE C 267 
 TRP   0.027   0.001   TRP B 455 
 HIS   0.003   0.001   HIS B 342 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 7452)
  covalent geometry    : angle       0.60753 (10173)
  hydrogen bonds       : bond        0.04244 (  483)
  hydrogen bonds       : angle       3.94982 ( 1362)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A  331 ARG cc_start: 0.7547 (mpp80) cc_final: 0.6153 (mmm160)
REVERT: A  332 ARG cc_start: 0.6594 (ttp-110) cc_final: 0.5673 (ttt90)
REVERT: A  505 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6233 (mp)
REVERT: B  224 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.6617 (mtm)
REVERT: B  331 ARG cc_start: 0.7423 (mpp80) cc_final: 0.6173 (mmm160)
REVERT: B  332 ARG cc_start: 0.6421 (ttp-110) cc_final: 0.5498 (ttt90)
REVERT: B  479 PHE cc_start: 0.8102 (t80) cc_final: 0.7770 (t80)
REVERT: C  264 ARG cc_start: 0.6635 (ttp-110) cc_final: 0.6231 (ttp-110)
REVERT: C  272 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7283 (mtt180)
  outliers start: 8
  outliers final: 3
  residues processed: 99
  average time/residue: 0.6581
  time to fit residues: 68.2422
Evaluate side-chains
  94 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain B residue  224 MET
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain C residue  421 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 74 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 88 optimal weight:    0.6980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.152708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.107481 restraints weight = 31231.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 5.56
r_work: 0.2703 rms_B_bonded: 5.37 restraints_weight: 2.0000
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2777
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2777
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7452  Z= 0.121
  Angle     :  0.557   7.295  10173  Z= 0.271
  Chirality :  0.038   0.121   1191
  Planarity :  0.004   0.030   1218
  Dihedral  : 14.450 148.161   1173
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 26.93 %
    Favored  : 71.18 %
  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:  1.15 (0.29), residues: 936
  helix:  1.12 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop : -0.03 (0.46), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 264 
 TYR   0.016   0.001   TYR A 259 
 PHE   0.016   0.001   PHE C 267 
 TRP   0.026   0.001   TRP B 455 
 HIS   0.002   0.001   HIS B 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7452)
  covalent geometry    : angle       0.55719 (10173)
  hydrogen bonds       : bond        0.03638 (  483)
  hydrogen bonds       : angle       3.79264 ( 1362)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  264 ARG cc_start: 0.6466 (ttp-110) cc_final: 0.6177 (mtm180)
REVERT: A  331 ARG cc_start: 0.7436 (mpp80) cc_final: 0.6047 (mmm160)
REVERT: A  332 ARG cc_start: 0.6518 (ttp-110) cc_final: 0.5606 (ttt90)
REVERT: A  421 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.7696 (m-80)
REVERT: A  505 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6171 (mp)
REVERT: B  224 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.6547 (mtm)
REVERT: B  331 ARG cc_start: 0.7395 (mpp80) cc_final: 0.6035 (mmm160)
REVERT: B  332 ARG cc_start: 0.6208 (ttp-110) cc_final: 0.5334 (ttt90)
REVERT: C  224 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.6338 (mmm)
REVERT: C  264 ARG cc_start: 0.6611 (ttp-110) cc_final: 0.6166 (ttp-110)
REVERT: C  272 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7256 (mtt180)
REVERT: C  421 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.7726 (m-80)
  outliers start: 10
  outliers final: 2
  residues processed: 97
  average time/residue: 0.6067
  time to fit residues: 61.7509
Evaluate side-chains
  98 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain B residue  224 MET
Chi-restraints excluded: chain B residue  421 PHE
Chi-restraints excluded: chain C residue  224 MET
Chi-restraints excluded: chain C residue  421 PHE
Chi-restraints excluded: chain C residue  495 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   chunk 57 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.152233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.106657 restraints weight = 27895.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 5.25
r_work: 0.2788 rms_B_bonded: 5.14 restraints_weight: 2.0000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2780
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2780
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7452  Z= 0.132
  Angle     :  0.562   6.401  10173  Z= 0.274
  Chirality :  0.038   0.125   1191
  Planarity :  0.004   0.030   1218
  Dihedral  : 14.279 145.694   1173
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 26.93 %
    Favored  : 71.18 %
  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:  1.25 (0.29), residues: 936
  helix:  1.19 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop :  0.06 (0.46), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 264 
 TYR   0.015   0.001   TYR A 259 
 PHE   0.016   0.001   PHE C 267 
 TRP   0.026   0.001   TRP B 455 
 HIS   0.002   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7452)
  covalent geometry    : angle       0.56245 (10173)
  hydrogen bonds       : bond        0.03743 (  483)
  hydrogen bonds       : angle       3.80444 ( 1362)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  264 ARG cc_start: 0.6426 (ttp-110) cc_final: 0.6174 (mtm180)
REVERT: A  331 ARG cc_start: 0.7429 (mpp80) cc_final: 0.6087 (mmm160)
REVERT: A  332 ARG cc_start: 0.6439 (ttp-110) cc_final: 0.5532 (ttt90)
REVERT: A  421 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.7549 (m-80)
REVERT: A  505 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6047 (mp)
REVERT: B  224 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.6615 (mtm)
REVERT: B  331 ARG cc_start: 0.7421 (mpp80) cc_final: 0.5981 (mmm160)
REVERT: B  332 ARG cc_start: 0.6238 (ttp-110) cc_final: 0.5333 (ttt90)
REVERT: C  264 ARG cc_start: 0.6610 (ttp-110) cc_final: 0.6161 (ttp-110)
REVERT: C  272 ARG cc_start: 0.7505 (mtt180) cc_final: 0.7162 (mtt180)
REVERT: C  421 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.7583 (m-80)
  outliers start: 10
  outliers final: 2
  residues processed: 98
  average time/residue: 0.6091
  time to fit residues: 62.6491
Evaluate side-chains
  97 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain B residue  224 MET
Chi-restraints excluded: chain B residue  421 PHE
Chi-restraints excluded: chain B residue  489 SER
Chi-restraints excluded: chain C residue  421 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 91 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.152747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.107756 restraints weight = 27400.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 5.27
r_work: 0.2791 rms_B_bonded: 5.16 restraints_weight: 2.0000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2702
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2702
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7452  Z= 0.130
  Angle     :  0.564   6.261  10173  Z= 0.275
  Chirality :  0.038   0.125   1191
  Planarity :  0.004   0.030   1218
  Dihedral  : 14.151 143.823   1173
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 27.22 %
    Favored  : 71.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.29), residues: 936
  helix:  1.21 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop :  0.14 (0.47), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 264 
 TYR   0.015   0.001   TYR A 259 
 PHE   0.027   0.001   PHE B 479 
 TRP   0.026   0.001   TRP B 455 
 HIS   0.002   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7452)
  covalent geometry    : angle       0.56367 (10173)
  hydrogen bonds       : bond        0.03715 (  483)
  hydrogen bonds       : angle       3.80243 ( 1362)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  264 ARG cc_start: 0.6387 (ttp-110) cc_final: 0.6143 (mtm180)
REVERT: A  331 ARG cc_start: 0.7429 (mpp80) cc_final: 0.6047 (mmm160)
REVERT: A  332 ARG cc_start: 0.6351 (ttp-110) cc_final: 0.5450 (ttt90)
REVERT: A  421 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.7513 (m-80)
REVERT: A  505 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6061 (mp)
REVERT: B  224 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.6561 (mtm)
REVERT: B  331 ARG cc_start: 0.7378 (mpp80) cc_final: 0.6039 (mmm160)
REVERT: B  332 ARG cc_start: 0.6139 (ttp-110) cc_final: 0.5267 (ttt90)
REVERT: C  264 ARG cc_start: 0.6559 (ttp-110) cc_final: 0.6098 (ttp-110)
REVERT: C  272 ARG cc_start: 0.7391 (mtt180) cc_final: 0.7052 (mtt180)
REVERT: C  421 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.7477 (m-80)
  outliers start: 9
  outliers final: 2
  residues processed: 102
  average time/residue: 0.6111
  time to fit residues: 65.4817
Evaluate side-chains
  100 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain B residue  224 MET
Chi-restraints excluded: chain B residue  421 PHE
Chi-restraints excluded: chain B residue  489 SER
Chi-restraints excluded: chain C residue  421 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 61 optimal weight:    7.9990
   chunk 73 optimal weight:    8.9990
   chunk 65 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.152443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.107670 restraints weight = 19623.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 4.03
r_work: 0.2755 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2668
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2668 r_free = 0.2668    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2668 r_free = 0.2668    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2668
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7452  Z= 0.134
  Angle     :  0.570   6.813  10173  Z= 0.279
  Chirality :  0.038   0.125   1191
  Planarity :  0.003   0.030   1218
  Dihedral  : 14.066 142.228   1173
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 27.51 %
    Favored  : 71.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.29), residues: 936
  helix:  1.23 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop :  0.18 (0.47), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 264 
 TYR   0.015   0.001   TYR A 259 
 PHE   0.023   0.001   PHE C 479 
 TRP   0.026   0.001   TRP B 455 
 HIS   0.002   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7452)
  covalent geometry    : angle       0.57049 (10173)
  hydrogen bonds       : bond        0.03757 (  483)
  hydrogen bonds       : angle       3.81220 ( 1362)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A  331 ARG cc_start: 0.7478 (mpp80) cc_final: 0.6128 (mmm160)
REVERT: A  332 ARG cc_start: 0.6477 (ttp-110) cc_final: 0.5589 (ttt90)
REVERT: A  421 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.7566 (m-80)
REVERT: A  490 LEU cc_start: 0.8015 (tp) cc_final: 0.7630 (mm)
REVERT: A  505 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6098 (mp)
REVERT: B  331 ARG cc_start: 0.7424 (mpp80) cc_final: 0.6117 (mmm160)
REVERT: B  332 ARG cc_start: 0.6268 (ttp-110) cc_final: 0.5382 (ttt90)
REVERT: C  225 ARG cc_start: 0.7956 (mpt-90) cc_final: 0.7665 (mpt-90)
REVERT: C  264 ARG cc_start: 0.6635 (ttp-110) cc_final: 0.6169 (ttp-110)
REVERT: C  272 ARG cc_start: 0.7440 (mtt180) cc_final: 0.7098 (mtt180)
REVERT: C  421 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.7524 (m-80)
  outliers start: 7
  outliers final: 2
  residues processed: 100
  average time/residue: 0.5890
  time to fit residues: 61.7510
Evaluate side-chains
  101 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain B residue  421 PHE
Chi-restraints excluded: chain B residue  489 SER
Chi-restraints excluded: chain C residue  421 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 74 optimal weight:    0.2980
   chunk 83 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 84 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.153416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.108181 restraints weight = 24382.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 4.80
r_work: 0.2708 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7452  Z= 0.124
  Angle     :  0.561   7.136  10173  Z= 0.275
  Chirality :  0.038   0.124   1191
  Planarity :  0.003   0.030   1218
  Dihedral  : 13.942 140.760   1173
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 27.95 %
    Favored  : 70.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.29), residues: 936
  helix:  1.28 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop :  0.26 (0.48), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 264 
 TYR   0.013   0.001   TYR A 259 
 PHE   0.023   0.001   PHE C 479 
 TRP   0.025   0.001   TRP B 455 
 HIS   0.002   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7452)
  covalent geometry    : angle       0.56053 (10173)
  hydrogen bonds       : bond        0.03651 (  483)
  hydrogen bonds       : angle       3.77259 ( 1362)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2420.84 seconds
wall clock time: 41 minutes 54.21 seconds (2514.21 seconds total)