Starting phenix.real_space_refine
on Wed Mar 12 07:06:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7en0_31197/03_2025/7en0_31197.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7en0_31197/03_2025/7en0_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_2025/7en0_31197.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7en0_31197/03_2025/7en0_31197.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7en0_31197/03_2025/7en0_31197.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7en0_31197/03_2025/7en0_31197.cif"
  }
  resolution = 2.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 8}
          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: {'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 8}
          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:
    C, B
  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: 5.42, per 1000 atoms: 0.75
  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: 1.89
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  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: 0.88
  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: 1.90

  Time building geometry restraints manager: 2.21 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:                  0.000
  Normalize map: mean=0, sd=1:             0.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.920
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.010
-------------------------------------------------------------------------------
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= 0.455
  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 : 8.99
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.26 (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
 TRP   0.008   0.001   TRP B 215 
 HIS   0.005   0.001   HIS B 374 
 PHE   0.017   0.001   PHE A 421 
 TYR   0.007   0.001   TYR C 400 
 ARG   0.015   0.001   ARG A 225 

*********************** 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  : 0.741 
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: 0.7087 (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: 0.6176 (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: 0.7499 (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: 0.6321 (OUTLIER) cc_final: 0.6048 (mp)
  outliers start: 30
  outliers final: 7
  residues processed: 148
  average time/residue: 1.1498
  time to fit residues: 179.8580
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  : 0.721 
-------------------------------------------------------------------------------
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 78 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 39 optimal weight:    0.1980
   chunk 24 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   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 374 HIS
C 374 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.155694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.110462 restraints weight = 26156.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 5.04
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3143
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.1575

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= 0.186
  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 : 8.86
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (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
 TRP   0.013   0.001   TRP B 455 
 HIS   0.004   0.001   HIS C 374 
 PHE   0.021   0.001   PHE B 260 
 TYR   0.019   0.002   TYR B 259 
 ARG   0.004   0.001   ARG C 264 

*********************** 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  : 0.742 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 ARG cc_start: 0.6295 (mtm-85) cc_final: 0.5994 (ttp-110)
REVERT: A  332 ARG cc_start: 0.5824 (ttp-110) cc_final: 0.5015 (ttt90)
REVERT: C  264 ARG cc_start: 0.6285 (mtm-85) cc_final: 0.6029 (mtm180)
REVERT: C  272 ARG cc_start: 0.7443 (mtt180) cc_final: 0.7119 (mtt180)
REVERT: C  482 ARG cc_start: 0.7660 (ttm170) cc_final: 0.7422 (ttm-80)
REVERT: C  501 VAL cc_start: 0.7921 (m) cc_final: 0.7671 (t)
REVERT: C  505 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5999 (mp)
  outliers start: 13
  outliers final: 3
  residues processed: 104
  average time/residue: 1.4405
  time to fit residues: 157.1553
Evaluate side-chains
  96 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
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 81 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0570
   chunk 41 optimal weight:    0.6980
   chunk 38 optimal weight:    9.9990
   chunk 65 optimal weight:    0.0670
   chunk 82 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.4436

-------------------------------------------------------------------------------
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 = 0.3751 r_free = 0.3751 target = 0.156186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.112410 restraints weight = 28903.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 5.88
r_work: 0.2788 rms_B_bonded: 5.53 restraints_weight: 2.0000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2701
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2700 r_free = 0.2700    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2700
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7452  Z= 0.156
  Angle     :  0.553  10.165  10173  Z= 0.268
  Chirality :  0.037   0.117   1191
  Planarity :  0.004   0.030   1218
  Dihedral  : 15.466 152.120   1175
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 23.29 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.28), residues: 936
  helix:  0.35 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop : -0.50 (0.45), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 455 
 HIS   0.002   0.001   HIS A 303 
 PHE   0.025   0.001   PHE C 267 
 TYR   0.016   0.001   TYR C 259 
 ARG   0.003   0.000   ARG B 331 

*********************** 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
  111 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 ARG cc_start: 0.6401 (mtm-85) cc_final: 0.6046 (ttp-110)
REVERT: A  331 ARG cc_start: 0.7450 (mpp80) cc_final: 0.6068 (mmm160)
REVERT: A  431 MET cc_start: 0.8093 (ttm) cc_final: 0.7628 (mtp)
REVERT: A  505 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6288 (mp)
REVERT: B  225 ARG cc_start: 0.8082 (mpt-90) cc_final: 0.7829 (mpt-90)
REVERT: B  314 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8329 (tt)
REVERT: C  272 ARG cc_start: 0.7783 (mtt180) cc_final: 0.7491 (mtt180)
REVERT: C  501 VAL cc_start: 0.7897 (m) cc_final: 0.7689 (t)
REVERT: C  505 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.6112 (mp)
  outliers start: 12
  outliers final: 1
  residues processed: 104
  average time/residue: 1.2352
  time to fit residues: 135.5974
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  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain B residue  314 LEU
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 78 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 8 optimal weight:    0.4980
   chunk 79 optimal weight:    0.9980
   chunk 7 optimal weight:   20.0000
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 348 ASN
C 234 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.149364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.104237 restraints weight = 25143.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 4.96
r_work: 0.2767 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2679
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2679 r_free = 0.2679    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7452  Z= 0.303
  Angle     :  0.619   9.578  10173  Z= 0.300
  Chirality :  0.040   0.133   1191
  Planarity :  0.004   0.031   1218
  Dihedral  : 15.081 148.832   1175
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 25.04 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.28), residues: 936
  helix:  0.43 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop : -0.50 (0.44), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 455 
 HIS   0.003   0.001   HIS B 342 
 PHE   0.023   0.002   PHE C 267 
 TYR   0.010   0.001   TYR C 259 
 ARG   0.006   0.001   ARG C 264 

*********************** 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
  113 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ARG cc_start: 0.7449 (mpp80) cc_final: 0.6138 (mmm160)
REVERT: A  332 ARG cc_start: 0.6533 (ttp-110) cc_final: 0.5596 (ttt90)
REVERT: A  505 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6159 (mp)
REVERT: B  249 SER cc_start: 0.8621 (t) cc_final: 0.8343 (m)
REVERT: B  314 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8420 (tt)
REVERT: B  331 ARG cc_start: 0.7452 (mpp80) cc_final: 0.6046 (mmm160)
REVERT: B  332 ARG cc_start: 0.6368 (ttp-110) cc_final: 0.5437 (ttt90)
REVERT: B  479 PHE cc_start: 0.8103 (t80) cc_final: 0.7896 (t80)
REVERT: C  224 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.6309 (mmm)
REVERT: C  227 LEU cc_start: 0.7329 (mt) cc_final: 0.7108 (mp)
REVERT: C  264 ARG cc_start: 0.6533 (ttp-110) cc_final: 0.6274 (ttp-110)
REVERT: C  272 ARG cc_start: 0.7741 (mtt180) cc_final: 0.7406 (mtt180)
REVERT: C  505 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5902 (mp)
  outliers start: 9
  outliers final: 1
  residues processed: 107
  average time/residue: 1.3394
  time to fit residues: 150.5440
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  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain C residue  224 MET
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 64 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 86 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9980
   chunk 55 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3711 r_free = 0.3711 target = 0.152417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.107208 restraints weight = 25513.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 4.87
r_work: 0.2797 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2745
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2745 r_free = 0.2745    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2744 r_free = 0.2744    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2744
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7452  Z= 0.188
  Angle     :  0.559   8.608  10173  Z= 0.271
  Chirality :  0.038   0.123   1191
  Planarity :  0.004   0.031   1218
  Dihedral  : 14.813 150.781   1175
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 26.06 %
    Favored  : 72.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.28), residues: 936
  helix:  0.82 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop : -0.45 (0.44), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 455 
 HIS   0.002   0.001   HIS B 342 
 PHE   0.020   0.001   PHE C 267 
 TYR   0.017   0.001   TYR A 259 
 ARG   0.005   0.000   ARG C 264 

*********************** 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
  108 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ARG cc_start: 0.7426 (mpp80) cc_final: 0.6107 (mmm160)
REVERT: A  332 ARG cc_start: 0.6414 (ttp-110) cc_final: 0.5486 (ttt90)
REVERT: A  421 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.7725 (m-80)
REVERT: A  437 MET cc_start: 0.8206 (mtm) cc_final: 0.7995 (mtp)
REVERT: A  505 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6207 (mp)
REVERT: B  224 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.6493 (mtm)
REVERT: B  249 SER cc_start: 0.8622 (t) cc_final: 0.8407 (m)
REVERT: B  331 ARG cc_start: 0.7412 (mpp80) cc_final: 0.6115 (mmm160)
REVERT: B  479 PHE cc_start: 0.8195 (t80) cc_final: 0.7984 (t80)
REVERT: C  264 ARG cc_start: 0.6551 (ttp-110) cc_final: 0.6189 (ttp-110)
REVERT: C  272 ARG cc_start: 0.7735 (mtt180) cc_final: 0.7402 (mtt180)
  outliers start: 10
  outliers final: 2
  residues processed: 104
  average time/residue: 1.2379
  time to fit residues: 135.6449
Evaluate side-chains
  102 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
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  442 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 4 optimal weight:    0.1980
   chunk 55 optimal weight:   10.0000
   chunk 40 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0970
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 = 0.3743 r_free = 0.3743 target = 0.155466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.111092 restraints weight = 26864.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 5.30
r_work: 0.2778 rms_B_bonded: 5.12 restraints_weight: 2.0000
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2734
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2734 r_free = 0.2734    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2734 r_free = 0.2734    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2734
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7452  Z= 0.159
  Angle     :  0.539   7.385  10173  Z= 0.262
  Chirality :  0.037   0.121   1191
  Planarity :  0.003   0.030   1218
  Dihedral  : 14.419 150.524   1173
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 26.78 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.29), residues: 936
  helix:  1.16 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop : -0.25 (0.45), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 455 
 HIS   0.002   0.001   HIS B 303 
 PHE   0.017   0.001   PHE C 267 
 TYR   0.007   0.001   TYR B 436 
 ARG   0.006   0.000   ARG C 264 

*********************** 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
  107 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.647 
Fit side-chains
REVERT: A  260 PHE cc_start: 0.7452 (t80) cc_final: 0.7179 (t80)
REVERT: A  264 ARG cc_start: 0.6455 (ttp-110) cc_final: 0.5809 (ttp-110)
REVERT: A  331 ARG cc_start: 0.7399 (mpp80) cc_final: 0.6115 (mmm160)
REVERT: A  332 ARG cc_start: 0.6298 (ttp-110) cc_final: 0.5419 (ttt90)
REVERT: A  421 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7541 (m-80)
REVERT: A  431 MET cc_start: 0.8096 (ttm) cc_final: 0.7506 (mtp)
REVERT: A  437 MET cc_start: 0.8178 (mtm) cc_final: 0.7971 (mtp)
REVERT: A  505 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6332 (mp)
REVERT: B  331 ARG cc_start: 0.7344 (mpp80) cc_final: 0.5948 (mmm160)
REVERT: C  264 ARG cc_start: 0.6632 (ttp-110) cc_final: 0.6201 (ttp-110)
REVERT: C  272 ARG cc_start: 0.7517 (mtt180) cc_final: 0.7174 (mtt180)
  outliers start: 7
  outliers final: 0
  residues processed: 105
  average time/residue: 1.2437
  time to fit residues: 137.8396
Evaluate side-chains
  96 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 94
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  505 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 78 optimal weight:    0.4980
   chunk 89 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0060
   chunk 65 optimal weight:    7.9990
   overall best weight:    0.6798

-------------------------------------------------------------------------------
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 = 0.3729 r_free = 0.3729 target = 0.154165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.108993 restraints weight = 22799.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 4.74
r_work: 0.2843 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2706 r_free = 0.2706    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2706 r_free = 0.2706    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7452  Z= 0.175
  Angle     :  0.541   6.535  10173  Z= 0.265
  Chirality :  0.037   0.124   1191
  Planarity :  0.003   0.029   1218
  Dihedral  : 14.248 148.176   1173
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.29), residues: 936
  helix:  1.28 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop : -0.09 (0.45), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 455 
 HIS   0.002   0.001   HIS B 303 
 PHE   0.023   0.001   PHE B 479 
 TYR   0.007   0.001   TYR A 436 
 ARG   0.004   0.000   ARG C 264 

*********************** 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
  106 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.737 
Fit side-chains
REVERT: A  260 PHE cc_start: 0.7268 (t80) cc_final: 0.6952 (t80)
REVERT: A  264 ARG cc_start: 0.6455 (ttp-110) cc_final: 0.5837 (ttp-110)
REVERT: A  331 ARG cc_start: 0.7390 (mpp80) cc_final: 0.6072 (mmm160)
REVERT: A  332 ARG cc_start: 0.6240 (ttp-110) cc_final: 0.5362 (ttt90)
REVERT: A  421 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7423 (m-80)
REVERT: A  498 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7165 (mp)
REVERT: A  505 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6016 (mp)
REVERT: B  224 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.6601 (mtm)
REVERT: B  331 ARG cc_start: 0.7308 (mpp80) cc_final: 0.5956 (mmm160)
REVERT: C  224 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.6364 (mmm)
REVERT: C  264 ARG cc_start: 0.6465 (ttp-110) cc_final: 0.6025 (ttp-110)
REVERT: C  272 ARG cc_start: 0.7337 (mtt180) cc_final: 0.7011 (mtt180)
REVERT: C  421 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7485 (m-80)
  outliers start: 9
  outliers final: 1
  residues processed: 101
  average time/residue: 1.1668
  time to fit residues: 124.9036
Evaluate side-chains
  101 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  498 LEU
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 65 optimal weight:    8.9990
   chunk 50 optimal weight:    0.4980
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3721 r_free = 0.3721 target = 0.153546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.108414 restraints weight = 26025.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 4.98
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3096
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2825

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= 0.188
  Angle     :  0.550   5.779  10173  Z= 0.269
  Chirality :  0.038   0.125   1191
  Planarity :  0.003   0.029   1218
  Dihedral  : 14.121 146.342   1173
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 26.93 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.29), residues: 936
  helix:  1.30 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop : -0.01 (0.46), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 455 
 HIS   0.002   0.001   HIS A 374 
 PHE   0.021   0.001   PHE C 479 
 TYR   0.006   0.001   TYR C 252 
 ARG   0.004   0.000   ARG C 264 

*********************** 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
  105 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.681 
Fit side-chains
REVERT: A  260 PHE cc_start: 0.7047 (t80) cc_final: 0.6747 (t80)
REVERT: A  264 ARG cc_start: 0.6435 (ttp-110) cc_final: 0.5772 (ttp-110)
REVERT: A  331 ARG cc_start: 0.7253 (mpp80) cc_final: 0.5942 (mmm160)
REVERT: A  332 ARG cc_start: 0.6076 (ttp-110) cc_final: 0.5277 (ttt90)
REVERT: A  421 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7323 (m-80)
REVERT: A  498 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7289 (mp)
REVERT: A  505 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6040 (mp)
REVERT: B  331 ARG cc_start: 0.7148 (mpp80) cc_final: 0.5798 (mmm160)
REVERT: B  332 ARG cc_start: 0.5715 (ttp-110) cc_final: 0.4982 (ttt90)
REVERT: C  264 ARG cc_start: 0.6336 (ttp-110) cc_final: 0.5844 (ttp-110)
REVERT: C  272 ARG cc_start: 0.7223 (mtt180) cc_final: 0.6836 (mtt180)
REVERT: C  421 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7324 (m-80)
  outliers start: 11
  outliers final: 3
  residues processed: 100
  average time/residue: 1.2334
  time to fit residues: 130.2059
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  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain B residue  421 PHE
Chi-restraints excluded: chain C residue  294 LEU
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 26 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 7 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0050
   chunk 83 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.6394

-------------------------------------------------------------------------------
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 = 0.3735 r_free = 0.3735 target = 0.154805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.109145 restraints weight = 28560.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 5.39
r_work: 0.2735 rms_B_bonded: 5.37 restraints_weight: 2.0000
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2687
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2687 r_free = 0.2687    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2687 r_free = 0.2687    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2687
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7452  Z= 0.174
  Angle     :  0.542   5.772  10173  Z= 0.267
  Chirality :  0.037   0.123   1191
  Planarity :  0.003   0.029   1218
  Dihedral  : 13.972 144.882   1173
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.29), residues: 936
  helix:  1.37 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop :  0.13 (0.47), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 455 
 HIS   0.002   0.001   HIS B 303 
 PHE   0.010   0.001   PHE C 226 
 TYR   0.006   0.001   TYR C 252 
 ARG   0.004   0.000   ARG C 264 

*********************** 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
  112 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.758 
Fit side-chains
REVERT: A  249 SER cc_start: 0.8511 (t) cc_final: 0.8266 (m)
REVERT: A  331 ARG cc_start: 0.7438 (mpp80) cc_final: 0.6109 (mmm160)
REVERT: A  332 ARG cc_start: 0.6347 (ttp-110) cc_final: 0.5461 (ttt90)
REVERT: A  421 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7504 (m-80)
REVERT: A  498 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7434 (mp)
REVERT: A  505 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6058 (mp)
REVERT: B  331 ARG cc_start: 0.7409 (mpp80) cc_final: 0.6103 (mmm160)
REVERT: C  264 ARG cc_start: 0.6616 (ttp-110) cc_final: 0.6152 (ttp-110)
REVERT: C  272 ARG cc_start: 0.7495 (mtt180) cc_final: 0.7151 (mtt90)
  outliers start: 8
  outliers final: 2
  residues processed: 108
  average time/residue: 1.1269
  time to fit residues: 128.8425
Evaluate side-chains
  106 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain B residue  421 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 74 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0870
   chunk 75 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0870
   overall best weight:    0.9338

-------------------------------------------------------------------------------
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 = 0.3716 r_free = 0.3716 target = 0.153053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.107164 restraints weight = 23504.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 4.62
r_work: 0.2724 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2679
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2679 r_free = 0.2679    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 = 0.2679 r_free = 0.2679    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2679
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
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= 0.206
  Angle     :  0.560   6.122  10173  Z= 0.275
  Chirality :  0.038   0.125   1191
  Planarity :  0.004   0.029   1218
  Dihedral  : 13.929 142.860   1173
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 27.37 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.29), residues: 936
  helix:  1.33 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop :  0.12 (0.47), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 455 
 HIS   0.002   0.001   HIS A 374 
 PHE   0.026   0.001   PHE B 479 
 TYR   0.007   0.001   TYR C 252 
 ARG   0.004   0.000   ARG C 264 

********************** 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
  105 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.661 
Fit side-chains
REVERT: A  331 ARG cc_start: 0.7427 (mpp80) cc_final: 0.6076 (mmm160)
REVERT: A  332 ARG cc_start: 0.6297 (ttp-110) cc_final: 0.5408 (ttt90)
REVERT: A  421 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7446 (m-80)
REVERT: A  498 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7278 (mp)
REVERT: A  505 LEU cc_start: 0.6411 (OUTLIER) cc_final: 0.6026 (mp)
REVERT: B  331 ARG cc_start: 0.7324 (mpp80) cc_final: 0.6010 (mmm160)
REVERT: B  332 ARG cc_start: 0.6072 (ttp-110) cc_final: 0.5217 (ttt90)
REVERT: C  264 ARG cc_start: 0.6477 (ttp-110) cc_final: 0.6014 (ttp-110)
REVERT: C  272 ARG cc_start: 0.7274 (mtt180) cc_final: 0.6959 (mtt180)
REVERT: C  421 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7354 (m-80)
  outliers start: 8
  outliers final: 3
  residues processed: 101
  average time/residue: 1.2380
  time to fit residues: 131.8720
Evaluate side-chains
  105 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain B residue  421 PHE
Chi-restraints excluded: chain C residue  294 LEU
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 9 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 37 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 91 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 86 optimal weight:    0.0020
   chunk 55 optimal weight:    0.3980
   overall best weight:    0.6588

-------------------------------------------------------------------------------
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 = 0.3733 r_free = 0.3733 target = 0.154512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.109101 restraints weight = 24197.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 4.69
r_work: 0.2827 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2719
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2719
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7452  Z= 0.175
  Angle     :  0.545   5.875  10173  Z= 0.269
  Chirality :  0.038   0.122   1191
  Planarity :  0.003   0.029   1218
  Dihedral  : 13.838 142.033   1173
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 27.07 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.29), residues: 936
  helix:  1.40 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop :  0.15 (0.47), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 455 
 HIS   0.002   0.001   HIS B 303 
 PHE   0.011   0.001   PHE B 260 
 TYR   0.006   0.001   TYR C 252 
 ARG   0.004   0.000   ARG C 264 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4987.75 seconds
wall clock time: 85 minutes 48.91 seconds (5148.91 seconds total)