Starting phenix.real_space_refine
on Fri Feb 14 14:05:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x15_21989/02_2025/6x15_21989.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x15_21989/02_2025/6x15_21989.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6x15_21989/02_2025/6x15_21989.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x15_21989/02_2025/6x15_21989.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x15_21989/02_2025/6x15_21989.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x15_21989/02_2025/6x15_21989.cif"
  }
  resolution = 3.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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: 7
    Type Number    sf(0)   Gaussians
     Hg      3     10.96       5
     P       9      5.49       5
     S      57      5.16       5
     Na      9      4.78       5
     C    6705      2.51       5
     N    1518      2.21       5
     O    1725      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10026
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 3112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3112
          Classifications: {'peptide': 419}
          Link IDs: {'PTRANS': 18, 'TRANS': 400}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 3112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3112
          Classifications: {'peptide': 419}
          Link IDs: {'PTRANS': 18, 'TRANS': 400}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 3112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3112
          Classifications: {'peptide': 419}
          Link IDs: {'PTRANS': 18, 'TRANS': 400}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 227
          Unusual residues: {' HG': 1, ' NA': 3, '6OU': 13}
          Inner-chain residues flagged as termini: ['pdbres="ASP A 504 "']
          Classifications: {'peptide': 1, 'undetermined': 17}
          Modifications used: {'COO': 1}
          Link IDs: {None: 17}
          Unresolved non-hydrogen bonds: 423
          Unresolved non-hydrogen angles: 483
          Unresolved non-hydrogen dihedrals: 423
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'6OU:plan-1': 12, '6OU:plan-2': 10, '6OU:plan-3': 10}
          Unresolved non-hydrogen planarities: 124
    Chain: "B"
      Number of atoms: 227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 227
          Unusual residues: {' HG': 1, ' NA': 3, '6OU': 13}
          Inner-chain residues flagged as termini: ['pdbres="ASP B 505 "']
          Classifications: {'peptide': 1, 'undetermined': 17}
          Modifications used: {'COO': 1}
          Link IDs: {None: 17}
          Unresolved non-hydrogen bonds: 423
          Unresolved non-hydrogen angles: 483
          Unresolved non-hydrogen dihedrals: 423
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'6OU:plan-1': 12, '6OU:plan-2': 10, '6OU:plan-3': 10}
          Unresolved non-hydrogen planarities: 124
    Chain: "C"
      Number of atoms: 227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 227
          Unusual residues: {' HG': 1, ' NA': 3, '6OU': 13}
          Inner-chain residues flagged as termini: ['pdbres="ASP C 505 "']
          Classifications: {'peptide': 1, 'undetermined': 17}
          Modifications used: {'COO': 1}
          Link IDs: {None: 17}
          Unresolved non-hydrogen bonds: 423
          Unresolved non-hydrogen angles: 483
          Unresolved non-hydrogen dihedrals: 423
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'6OU:plan-1': 12, '6OU:plan-2': 10, '6OU:plan-3': 10}
          Unresolved non-hydrogen planarities: 124
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2723  SG  CYS A 364      35.989  48.804  29.759  1.00 37.84           S
  ATOM   5835  SG  CYS B 364      60.154  73.323  29.832  1.00 37.84           S
  ATOM   8947  SG  CYS C 364      69.261  40.143  29.721  1.00 37.84           S

  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb="HG    HG A 505 " occ=0.30
    residue:
      pdb="HG    HG B 506 " occ=0.30
    residue:
      pdb="HG    HG C 506 " occ=0.30
  Time building chain proxies: 6.40, per 1000 atoms: 0.64
  Number of scatterers: 10026
  At special positions: 0
  Unit cell: (110.292, 111.353, 73.1745, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Hg      3     79.96
     S      57     16.00
     P       9     15.00
     Na      9     11.00
     O    1725      8.00
     N    1518      7.00
     C    6705      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.48
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2262

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 0 sheets defined
      83.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 9
      removed outlier: 3.911A  pdb=" N   ARG A   5 " --> pdb=" O   FME A   1 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 11 through 33
      removed outlier: 3.594A  pdb=" N   LEU A  22 " --> pdb=" O   ILE A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 43
      removed outlier: 3.764A  pdb=" N   VAL A  39 " --> pdb=" O   TYR A  35 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   HIS A  40 " --> pdb=" O   ALA A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.810A  pdb=" N   PHE A  50 " --> pdb=" O   PHE A  46 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LEU A  57 " --> pdb=" O   LEU A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 71
      removed outlier: 3.673A  pdb=" N   ILE A  61 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LEU A  66 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 107
      removed outlier: 3.713A  pdb=" N   LYS A  84 " --> pdb=" O   ARG A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 136
    Processing helix  chain 'A' and resid 141 through 148
    Processing helix  chain 'A' and resid 150 through 169
      removed outlier: 3.523A  pdb=" N   THR A 154 " --> pdb=" O   GLN A 150 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE A 156 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 221
      removed outlier: 3.825A  pdb=" N   GLN A 203 " --> pdb=" O   ASN A 199 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
      Proline residue:  A 206  - end of helix
      removed outlier: 3.724A  pdb=" N   TYR A 215 " --> pdb=" O   ALA A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 254
      removed outlier: 4.230A  pdb=" N   GLY A 226 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LYS A 230 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   TYR A 254 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 276
      removed outlier: 5.603A  pdb=" N   ASP A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
      removed outlier: 5.326A  pdb=" N   ALA A 268 " --> pdb=" O   HIS A 264 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   THR A 271 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 291
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 4.661A  pdb=" N   PHE A 301 " --> pdb=" O   GLY A 297 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU A 303 " --> pdb=" O   TYR A 299 " (cutoff:3.500A)
      Proline residue:  A 304  - end of helix
      removed outlier: 4.247A  pdb=" N   THR A 308 " --> pdb=" O   PRO A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 329
    Processing helix  chain 'A' and resid 338 through 352
      removed outlier: 3.664A  pdb=" N   VAL A 342 " --> pdb=" O   GLN A 338 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL A 346 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 371
      removed outlier: 3.562A  pdb=" N   MET A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   CYS A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   MET A 365 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL A 366 " --> pdb=" O   MET A 362 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL A 370 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLY A 371 " --> pdb=" O   LEU A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 388
      removed outlier: 3.611A  pdb=" N   ALA A 384 " --> pdb=" O   ALA A 380 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   MET A 385 " --> pdb=" O   ALA A 381 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ILE A 386 " --> pdb=" O   ALA A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 417
      removed outlier: 3.642A  pdb=" N   LEU A 393 " --> pdb=" O   ILE A 389 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   MET A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   GLY A 396 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASP A 405 " --> pdb=" O   ASN A 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 9
    Processing helix  chain 'B' and resid 11 through 33
      removed outlier: 3.595A  pdb=" N   LEU B  22 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 43
      removed outlier: 3.764A  pdb=" N   VAL B  39 " --> pdb=" O   TYR B  35 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   HIS B  40 " --> pdb=" O   ALA B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 57
      removed outlier: 3.811A  pdb=" N   PHE B  50 " --> pdb=" O   PHE B  46 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LEU B  57 " --> pdb=" O   LEU B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 71
      removed outlier: 3.673A  pdb=" N   ILE B  61 " --> pdb=" O   LEU B  57 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LEU B  66 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 107
      removed outlier: 3.713A  pdb=" N   LYS B  84 " --> pdb=" O   ARG B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 136
    Processing helix  chain 'B' and resid 141 through 148
    Processing helix  chain 'B' and resid 150 through 169
      removed outlier: 3.523A  pdb=" N   THR B 154 " --> pdb=" O   GLN B 150 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 221
      removed outlier: 3.826A  pdb=" N   GLN B 203 " --> pdb=" O   ASN B 199 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   TYR B 204 " --> pdb=" O   GLY B 200 " (cutoff:3.500A)
      Proline residue:  B 206  - end of helix
      removed outlier: 3.724A  pdb=" N   TYR B 215 " --> pdb=" O   ALA B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 254
      removed outlier: 4.230A  pdb=" N   GLY B 226 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LYS B 230 " --> pdb=" O   GLY B 226 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   VAL B 231 " --> pdb=" O   GLU B 227 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   TYR B 254 " --> pdb=" O   LEU B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 276
      removed outlier: 5.604A  pdb=" N   ASP B 267 " --> pdb=" O   LYS B 263 " (cutoff:3.500A)
      removed outlier: 5.327A  pdb=" N   ALA B 268 " --> pdb=" O   HIS B 264 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   THR B 271 " --> pdb=" O   ASP B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 291
    Processing helix  chain 'B' and resid 295 through 310
      removed outlier: 4.661A  pdb=" N   PHE B 301 " --> pdb=" O   GLY B 297 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU B 303 " --> pdb=" O   TYR B 299 " (cutoff:3.500A)
      Proline residue:  B 304  - end of helix
      removed outlier: 4.247A  pdb=" N   THR B 308 " --> pdb=" O   PRO B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 329
    Processing helix  chain 'B' and resid 338 through 352
      removed outlier: 3.664A  pdb=" N   VAL B 342 " --> pdb=" O   GLN B 338 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL B 346 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 371
      removed outlier: 3.562A  pdb=" N   MET B 362 " --> pdb=" O   ALA B 358 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   CYS B 364 " --> pdb=" O   ALA B 360 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   MET B 365 " --> pdb=" O   ILE B 361 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL B 366 " --> pdb=" O   MET B 362 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL B 370 " --> pdb=" O   VAL B 366 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLY B 371 " --> pdb=" O   LEU B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 388
      removed outlier: 3.611A  pdb=" N   ALA B 384 " --> pdb=" O   ALA B 380 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   MET B 385 " --> pdb=" O   ALA B 381 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ILE B 386 " --> pdb=" O   ALA B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 417
      removed outlier: 3.643A  pdb=" N   LEU B 393 " --> pdb=" O   ILE B 389 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   MET B 395 " --> pdb=" O   ALA B 391 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   GLY B 396 " --> pdb=" O   ILE B 392 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASP B 405 " --> pdb=" O   ASN B 401 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 9
    Processing helix  chain 'C' and resid 11 through 33
      removed outlier: 3.594A  pdb=" N   LEU C  22 " --> pdb=" O   ILE C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 43
      removed outlier: 3.764A  pdb=" N   VAL C  39 " --> pdb=" O   TYR C  35 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   HIS C  40 " --> pdb=" O   ALA C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 57
      removed outlier: 3.810A  pdb=" N   PHE C  50 " --> pdb=" O   PHE C  46 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LEU C  57 " --> pdb=" O   LEU C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 57 through 71
      removed outlier: 3.673A  pdb=" N   ILE C  61 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU C  66 " --> pdb=" O   VAL C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 107
      removed outlier: 3.714A  pdb=" N   LYS C  84 " --> pdb=" O   ARG C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 136
    Processing helix  chain 'C' and resid 141 through 148
    Processing helix  chain 'C' and resid 150 through 169
      removed outlier: 3.523A  pdb=" N   THR C 154 " --> pdb=" O   GLN C 150 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE C 156 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 221
      removed outlier: 3.825A  pdb=" N   GLN C 203 " --> pdb=" O   ASN C 199 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   TYR C 204 " --> pdb=" O   GLY C 200 " (cutoff:3.500A)
      Proline residue:  C 206  - end of helix
      removed outlier: 3.724A  pdb=" N   TYR C 215 " --> pdb=" O   ALA C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 254
      removed outlier: 4.230A  pdb=" N   GLY C 226 " --> pdb=" O   VAL C 222 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LYS C 230 " --> pdb=" O   GLY C 226 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL C 231 " --> pdb=" O   GLU C 227 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   TYR C 254 " --> pdb=" O   LEU C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 257 through 276
      removed outlier: 5.604A  pdb=" N   ASP C 267 " --> pdb=" O   LYS C 263 " (cutoff:3.500A)
      removed outlier: 5.326A  pdb=" N   ALA C 268 " --> pdb=" O   HIS C 264 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   THR C 271 " --> pdb=" O   ASP C 267 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 281 through 291
    Processing helix  chain 'C' and resid 295 through 310
      removed outlier: 4.661A  pdb=" N   PHE C 301 " --> pdb=" O   GLY C 297 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU C 303 " --> pdb=" O   TYR C 299 " (cutoff:3.500A)
      Proline residue:  C 304  - end of helix
      removed outlier: 4.247A  pdb=" N   THR C 308 " --> pdb=" O   PRO C 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 311 through 329
    Processing helix  chain 'C' and resid 338 through 352
      removed outlier: 3.664A  pdb=" N   VAL C 342 " --> pdb=" O   GLN C 338 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL C 346 " --> pdb=" O   VAL C 342 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 358 through 371
      removed outlier: 3.562A  pdb=" N   MET C 362 " --> pdb=" O   ALA C 358 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   CYS C 364 " --> pdb=" O   ALA C 360 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   MET C 365 " --> pdb=" O   ILE C 361 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL C 366 " --> pdb=" O   MET C 362 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL C 370 " --> pdb=" O   VAL C 366 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLY C 371 " --> pdb=" O   LEU C 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 376 through 388
      removed outlier: 3.612A  pdb=" N   ALA C 384 " --> pdb=" O   ALA C 380 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   MET C 385 " --> pdb=" O   ALA C 381 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ILE C 386 " --> pdb=" O   ALA C 382 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 389 through 417
      removed outlier: 3.643A  pdb=" N   LEU C 393 " --> pdb=" O   ILE C 389 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   MET C 395 " --> pdb=" O   ALA C 391 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   GLY C 396 " --> pdb=" O   ILE C 392 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASP C 405 " --> pdb=" O   ASN C 401 " (cutoff:3.500A)

    696 hydrogen bonds defined for protein.
    2088 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.85

  Time building geometry restraints manager: 2.83 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: 1479
        1.31 -     1.43: 2368
        1.43 -     1.55: 6057
        1.55 -     1.68: 134
        1.68 -     1.80: 108
  Bond restraints: 10146
  Sorted by residual:
  bond pdb=" C16 6OU B 509 "
       pdb=" O18 6OU B 509 "
    ideal  model  delta    sigma   weight residual
    1.327  1.419 -0.092 2.00e-02 2.50e+03 2.14e+01
  bond pdb=" C16 6OU C 509 "
       pdb=" O18 6OU C 509 "
    ideal  model  delta    sigma   weight residual
    1.327  1.419 -0.092 2.00e-02 2.50e+03 2.14e+01
  bond pdb=" C16 6OU A 508 "
       pdb=" O18 6OU A 508 "
    ideal  model  delta    sigma   weight residual
    1.327  1.419 -0.092 2.00e-02 2.50e+03 2.13e+01
  bond pdb=" C16 6OU C 508 "
       pdb=" O18 6OU C 508 "
    ideal  model  delta    sigma   weight residual
    1.327  1.416 -0.089 2.00e-02 2.50e+03 1.98e+01
  bond pdb=" C16 6OU A 507 "
       pdb=" O18 6OU A 507 "
    ideal  model  delta    sigma   weight residual
    1.327  1.416 -0.089 2.00e-02 2.50e+03 1.96e+01
  ... (remaining 10141 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.11: 13033
        3.11 -     6.22: 527
        6.22 -     9.33: 42
        9.33 -    12.45: 15
       12.45 -    15.56: 9
  Bond angle restraints: 13626
  Sorted by residual:
  angle pdb=" O22 6OU B 508 "
        pdb=" P23 6OU B 508 "
        pdb=" O26 6OU B 508 "
      ideal   model   delta    sigma   weight residual
      93.95  109.51  -15.56 3.00e+00 1.11e-01 2.69e+01
  angle pdb=" O22 6OU A 507 "
        pdb=" P23 6OU A 507 "
        pdb=" O26 6OU A 507 "
      ideal   model   delta    sigma   weight residual
      93.95  109.48  -15.53 3.00e+00 1.11e-01 2.68e+01
  angle pdb=" O22 6OU C 508 "
        pdb=" P23 6OU C 508 "
        pdb=" O26 6OU C 508 "
      ideal   model   delta    sigma   weight residual
      93.95  109.47  -15.52 3.00e+00 1.11e-01 2.68e+01
  angle pdb=" O22 6OU A 508 "
        pdb=" P23 6OU A 508 "
        pdb=" O26 6OU A 508 "
      ideal   model   delta    sigma   weight residual
      93.95  109.30  -15.35 3.00e+00 1.11e-01 2.62e+01
  angle pdb=" O22 6OU C 509 "
        pdb=" P23 6OU C 509 "
        pdb=" O26 6OU C 509 "
      ideal   model   delta    sigma   weight residual
      93.95  109.25  -15.30 3.00e+00 1.11e-01 2.60e+01
  ... (remaining 13621 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.10: 5808
       34.10 -    68.20: 234
       68.20 -   102.30: 48
      102.30 -   136.40: 18
      136.40 -   170.50: 9
  Dihedral angle restraints: 6117
    sinusoidal: 2547
      harmonic: 3570
  Sorted by residual:
  dihedral pdb=" C19 6OU A 507 "
           pdb=" C20 6OU A 507 "
           pdb=" C21 6OU A 507 "
           pdb=" O22 6OU A 507 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.00  130.50  170.50     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" C19 6OU B 508 "
           pdb=" C20 6OU B 508 "
           pdb=" C21 6OU B 508 "
           pdb=" O22 6OU B 508 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.00  130.52  170.48     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" C19 6OU C 508 "
           pdb=" C20 6OU C 508 "
           pdb=" C21 6OU C 508 "
           pdb=" O22 6OU C 508 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.00  130.52  170.48     1      3.00e+01 1.11e-03 2.12e+01
  ... (remaining 6114 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1187
       0.049 -    0.098: 349
       0.098 -    0.146: 81
       0.146 -    0.195: 13
       0.195 -    0.244: 8
  Chirality restraints: 1638
  Sorted by residual:
  chirality pdb=" C20 6OU C 509 "
            pdb=" C19 6OU C 509 "
            pdb=" C21 6OU C 509 "
            pdb=" O30 6OU C 509 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.59   -0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" C20 6OU B 509 "
            pdb=" C19 6OU B 509 "
            pdb=" C21 6OU B 509 "
            pdb=" O30 6OU B 509 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.59   -0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" C20 6OU A 508 "
            pdb=" C19 6OU A 508 "
            pdb=" C21 6OU A 508 "
            pdb=" O30 6OU A 508 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.59   -0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 1635 not shown)

  Planarity restraints: 1626
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  44 "    0.042 5.00e-02 4.00e+02   6.24e-02 6.22e+00
        pdb=" N   PRO C  45 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO C  45 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C  45 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  44 "    0.042 5.00e-02 4.00e+02   6.22e-02 6.19e+00
        pdb=" N   PRO A  45 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A  45 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A  45 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  44 "   -0.042 5.00e-02 4.00e+02   6.22e-02 6.18e+00
        pdb=" N   PRO B  45 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO B  45 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B  45 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1623 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2653
        2.80 -     3.33: 8942
        3.33 -     3.85: 16672
        3.85 -     4.38: 19443
        4.38 -     4.90: 34999
  Nonbonded interactions: 82709
  Sorted by model distance:
  nonbonded pdb=" O   ALA C 348 "
            pdb=" OG1 THR C 352 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   ALA A 348 "
            pdb=" OG1 THR A 352 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   ALA B 348 "
            pdb=" OG1 THR B 352 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OG1 THR B 334 "
            pdb=" O25 6OU B 509 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" OG1 THR A 334 "
            pdb=" O25 6OU A 508 "
     model   vdw
     2.302 3.040
  ... (remaining 82704 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: 0.03
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 419 or resid 502 through 503 or resid 507 throug \ 
h 508 or resid 510 through 514 or (resid 515 through 518 and (name C01 or name C \ 
02 or name C03 or name C04 or name C05 or name C06))))
  selection = (chain 'B' and (resid 1 through 419 or resid 502 through 503 or (resid 507 and ( \ 
name C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 \ 
 or name C08 or name C09 or name C10 or name C11 or name C12 or name C13 or name \ 
 C14 or name C15 or name C16 or name C19 or name C20 or name C21 or name C27 or  \ 
name C28 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 \ 
 or name C38 or name C39 or name C40 or name N29 or name O17 or name O18 or name \ 
 O22 or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)) o \ 
r (resid 508 and (name C10 or name C11 or name C12 or name C13 or name C14 or na \ 
me C15 or name C16 or name C19 or name C20 or name C21 or name C27 or name C28 o \ 
r name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 
38 or name N29 or name O17 or name O18 or name O22 or name O24 or name O25 or na \ 
me O26 or name O30 or name O32 or name P23)) or (resid 510 through 511 and (name \ 
 C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or  \ 
name C08 or name C09 or name C10 or name C11 or name C12)) or (resid 512 and (na \ 
me C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 o \ 
r name C08 or name C09 or name C10)) or (resid 513 through 518 and (name C01 or  \ 
name C02 or name C03 or name C04 or name C05 or name C06))))
  selection = (chain 'C' and (resid 1 through 419 or resid 502 through 503 or (resid 507 and ( \ 
name C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 \ 
 or name C08 or name C09 or name C10 or name C11 or name C12 or name C13 or name \ 
 C14 or name C15 or name C16 or name C19 or name C20 or name C21 or name C27 or  \ 
name C28 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 \ 
 or name C38 or name C39 or name C40 or name N29 or name O17 or name O18 or name \ 
 O22 or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)) o \ 
r (resid 508 and (name C10 or name C11 or name C12 or name C13 or name C14 or na \ 
me C15 or name C16 or name C19 or name C20 or name C21 or name C27 or name C28 o \ 
r name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 
38 or name N29 or name O17 or name O18 or name O22 or name O24 or name O25 or na \ 
me O26 or name O30 or name O32 or name P23)) or (resid 510 through 511 and (name \ 
 C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or  \ 
name C08 or name C09 or name C10 or name C11 or name C12)) or (resid 512 and (na \ 
me C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 o \ 
r name C08 or name C09 or name C10)) or (resid 513 through 518 and (name C01 or  \ 
name C02 or name C03 or name C04 or name C05 or name C06))))
}

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=0.30 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.720
  Find NCS groups from input model:        0.480
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
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      :  0.009   0.092  10146  Z= 0.581
  Angle     :  1.257  15.557  13626  Z= 0.551
  Chirality :  0.050   0.244   1638
  Planarity :  0.009   0.062   1626
  Dihedral  : 21.311 170.496   3855
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  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: -3.80 (0.17), residues: 1248
  helix: -2.29 (0.11), residues: 1029
  sheet:  None (None), residues: 0
  loop : -2.37 (0.33), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 114 
 PHE   0.020   0.002   PHE C 323 
 TYR   0.021   0.002   TYR C 299 
 ARG   0.002   0.000   ARG A 105 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 1.022 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8070 (t80) cc_final: 0.7831 (t80)
REVERT: A  132 HIS cc_start: 0.7939 (m90) cc_final: 0.7641 (m-70)
REVERT: A  136 ASP cc_start: 0.8316 (m-30) cc_final: 0.8115 (m-30)
REVERT: A  202 MET cc_start: 0.9219 (mmm) cc_final: 0.8987 (mmp)
REVERT: B   18 ILE cc_start: 0.9086 (pt) cc_final: 0.8791 (pt)
REVERT: B  185 ASP cc_start: 0.8227 (m-30) cc_final: 0.7771 (m-30)
REVERT: B  267 ASP cc_start: 0.7680 (m-30) cc_final: 0.7465 (m-30)
REVERT: C  136 ASP cc_start: 0.8314 (m-30) cc_final: 0.8036 (m-30)
REVERT: C  194 MET cc_start: 0.9080 (mmm) cc_final: 0.8861 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.2776
  time to fit residues: 61.2276
Evaluate side-chains
  115 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    0.3980
   chunk 93 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 62 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0770
   chunk 71 optimal weight:    0.6980
   chunk 111 optimal weight:    2.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A 121 GLN
A 242 GLN
A 337 GLN
B 121 GLN
B 242 GLN
B 337 GLN
B 338 GLN
C 121 GLN
C 242 GLN
C 337 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.105532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.087371 restraints weight = 11985.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.2884 rms_B_bonded: 1.33
r_work: 0.2767 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2640 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2624 r_free = 0.2624    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2624
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10146  Z= 0.156
  Angle     :  0.531   6.510  13626  Z= 0.270
  Chirality :  0.037   0.124   1638
  Planarity :  0.005   0.046   1626
  Dihedral  : 20.747 178.645   1863
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  8.26 %
    Favored  : 90.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.92 (0.22), residues: 1248
  helix: -0.16 (0.15), residues: 1053
  sheet:  None (None), residues: 0
  loop : -2.49 (0.34), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B 114 
 PHE   0.010   0.001   PHE A 323 
 TYR   0.024   0.001   TYR B 299 
 ARG   0.003   0.000   ARG A   5 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 1.059 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8312 (t80) cc_final: 0.8111 (t80)
REVERT: B   18 ILE cc_start: 0.8859 (pt) cc_final: 0.8656 (pt)
REVERT: B   59 MET cc_start: 0.9056 (mmm) cc_final: 0.8834 (mmp)
REVERT: B   77 ARG cc_start: 0.8505 (ptp-170) cc_final: 0.8232 (ptm160)
REVERT: B  136 ASP cc_start: 0.8789 (m-30) cc_final: 0.8559 (m-30)
REVERT: B  185 ASP cc_start: 0.8763 (m-30) cc_final: 0.8472 (m-30)
REVERT: C  136 ASP cc_start: 0.8702 (m-30) cc_final: 0.8131 (m-30)
  outliers start: 9
  outliers final: 6
  residues processed: 139
  average time/residue: 0.2184
  time to fit residues: 43.3419
Evaluate side-chains
  126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  385 MET
Chi-restraints excluded: chain B residue  338 GLN
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  267 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 69 optimal weight:    0.2980
   chunk 71 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
A 338 GLN
B 338 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.103150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.085044 restraints weight = 12595.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 1.36
r_work: 0.2723 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2595 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2595
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2618
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2618 r_free = 0.2618    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2617 r_free = 0.2617    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  10146  Z= 0.182
  Angle     :  0.518   6.075  13626  Z= 0.262
  Chirality :  0.038   0.124   1638
  Planarity :  0.005   0.044   1626
  Dihedral  : 18.410 176.204   1863
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  8.87 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.11 (0.24), residues: 1248
  helix:  0.50 (0.16), residues: 1059
  sheet:  None (None), residues: 0
  loop : -1.88 (0.38), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.011   0.001   PHE C 323 
 TYR   0.021   0.001   TYR B 299 
 ARG   0.003   0.000   ARG A   5 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.958 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8277 (t80) cc_final: 0.8059 (t80)
REVERT: B    5 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7545 (mtm110)
REVERT: B  136 ASP cc_start: 0.8735 (m-30) cc_final: 0.8475 (m-30)
REVERT: C  136 ASP cc_start: 0.8687 (m-30) cc_final: 0.8140 (m-30)
  outliers start: 9
  outliers final: 6
  residues processed: 130
  average time/residue: 0.2233
  time to fit residues: 41.1185
Evaluate side-chains
  128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 122
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  385 MET
Chi-restraints excluded: chain B residue  323 PHE
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  241 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   chunk 106 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.100651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.082596 restraints weight = 12587.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 1.35
r_work: 0.2691 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2564 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2564
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2531
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2531 r_free = 0.2531    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2530 r_free = 0.2530    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2530
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.2014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10146  Z= 0.243
  Angle     :  0.542   6.004  13626  Z= 0.274
  Chirality :  0.039   0.125   1638
  Planarity :  0.005   0.042   1626
  Dihedral  : 17.746 173.807   1863
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  9.79 %
    Favored  : 89.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.52 (0.24), residues: 1248
  helix:  0.75 (0.16), residues: 1068
  sheet:  None (None), residues: 0
  loop : -1.66 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 114 
 PHE   0.014   0.001   PHE C 323 
 TYR   0.023   0.001   TYR B 299 
 ARG   0.003   0.000   ARG C   5 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 1.086 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8412 (t80) cc_final: 0.8169 (t80)
REVERT: B  136 ASP cc_start: 0.8802 (m-30) cc_final: 0.8566 (m-30)
REVERT: B  224 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8160 (m)
REVERT: B  267 ASP cc_start: 0.8244 (m-30) cc_final: 0.7999 (m-30)
REVERT: C  136 ASP cc_start: 0.8722 (m-30) cc_final: 0.8194 (m-30)
  outliers start: 11
  outliers final: 7
  residues processed: 133
  average time/residue: 0.2386
  time to fit residues: 44.6698
Evaluate side-chains
  126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  385 MET
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  224 VAL
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  505 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 121 optimal weight:    3.9990
   chunk 114 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 120 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3104 r_free = 0.3104 target = 0.102088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.084040 restraints weight = 12559.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 1.35
r_work: 0.2688 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2562 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2562
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2589 r_free = 0.2589    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2589 r_free = 0.2589    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10146  Z= 0.181
  Angle     :  0.505   5.933  13626  Z= 0.256
  Chirality :  0.038   0.125   1638
  Planarity :  0.004   0.042   1626
  Dihedral  : 16.899 173.359   1863
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 10.30 %
    Favored  : 88.58 %
  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:  0.91 (0.24), residues: 1248
  helix:  1.06 (0.16), residues: 1050
  sheet:  None (None), residues: 0
  loop : -1.61 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 114 
 PHE   0.010   0.001   PHE C 323 
 TYR   0.020   0.001   TYR C 299 
 ARG   0.004   0.000   ARG A   5 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 1.081 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8348 (t80) cc_final: 0.8125 (t80)
REVERT: B  136 ASP cc_start: 0.8674 (m-30) cc_final: 0.8443 (m-30)
REVERT: B  267 ASP cc_start: 0.8111 (m-30) cc_final: 0.7896 (m-30)
REVERT: C  136 ASP cc_start: 0.8635 (m-30) cc_final: 0.8166 (m-30)
  outliers start: 11
  outliers final: 8
  residues processed: 131
  average time/residue: 0.2269
  time to fit residues: 42.1318
Evaluate side-chains
  128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain A residue  385 MET
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  323 PHE
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  241 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9990
   chunk 85 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 117 optimal weight:    0.0470
   chunk 32 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 = 0.3124 r_free = 0.3124 target = 0.103496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.085523 restraints weight = 12521.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 1.35
r_work: 0.2739 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2614 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2598
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2598 r_free = 0.2598    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2598 r_free = 0.2598    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2598
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10146  Z= 0.156
  Angle     :  0.493   5.845  13626  Z= 0.249
  Chirality :  0.037   0.123   1638
  Planarity :  0.004   0.040   1626
  Dihedral  : 16.377 172.965   1863
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.91 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.24), residues: 1248
  helix:  1.37 (0.17), residues: 1029
  sheet:  None (None), residues: 0
  loop : -1.21 (0.38), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B 114 
 PHE   0.007   0.001   PHE C 210 
 TYR   0.018   0.001   TYR C 299 
 ARG   0.004   0.000   ARG B   5 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.963 
Fit side-chains
REVERT: B  136 ASP cc_start: 0.8725 (m-30) cc_final: 0.8479 (m-30)
REVERT: B  194 MET cc_start: 0.9413 (mmp) cc_final: 0.9148 (mmp)
REVERT: C  136 ASP cc_start: 0.8651 (m-30) cc_final: 0.8214 (m-30)
  outliers start: 10
  outliers final: 8
  residues processed: 130
  average time/residue: 0.2229
  time to fit residues: 41.0499
Evaluate side-chains
  125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain A residue  385 MET
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  323 PHE
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  241 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 93 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0980
   chunk 25 optimal weight:    3.9990
   chunk 92 optimal weight:    0.6980
   chunk 88 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.103855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.085800 restraints weight = 12788.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 1.37
r_work: 0.2743 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2616 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2580
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2580 r_free = 0.2580    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2580 r_free = 0.2580    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2580
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10146  Z= 0.159
  Angle     :  0.489   5.855  13626  Z= 0.248
  Chirality :  0.037   0.124   1638
  Planarity :  0.004   0.039   1626
  Dihedral  : 15.990 172.205   1863
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 11.11 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.58 (0.24), residues: 1248
  helix:  1.49 (0.16), residues: 1032
  sheet:  None (None), residues: 0
  loop : -0.99 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 114 
 PHE   0.008   0.001   PHE A 323 
 TYR   0.019   0.001   TYR A 299 
 ARG   0.004   0.000   ARG B   5 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 1.086 
Fit side-chains
REVERT: B  136 ASP cc_start: 0.8712 (m-30) cc_final: 0.8463 (m-30)
REVERT: B  194 MET cc_start: 0.9397 (mmp) cc_final: 0.9144 (mmp)
REVERT: C  136 ASP cc_start: 0.8579 (m-30) cc_final: 0.8167 (m-30)
  outliers start: 12
  outliers final: 8
  residues processed: 132
  average time/residue: 0.2337
  time to fit residues: 44.0965
Evaluate side-chains
  125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain A residue  385 MET
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  224 VAL
Chi-restraints excluded: chain C residue  241 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 12 optimal weight:    0.0170
   chunk 28 optimal weight:    0.7980
   chunk 41 optimal weight:    7.9990
   chunk 108 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 116 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0050
   chunk 119 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.4832

-------------------------------------------------------------------------------
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 = 0.3149 r_free = 0.3149 target = 0.105232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.087330 restraints weight = 12765.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 1.37
r_work: 0.2758 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2632 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2599
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2599 r_free = 0.2599    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2599 r_free = 0.2599    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2599
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  10146  Z= 0.143
  Angle     :  0.478   5.764  13626  Z= 0.242
  Chirality :  0.037   0.124   1638
  Planarity :  0.004   0.039   1626
  Dihedral  : 15.499 171.032   1863
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 11.52 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.70 (0.24), residues: 1248
  helix:  1.61 (0.16), residues: 1041
  sheet:  None (None), residues: 0
  loop : -1.25 (0.39), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B 114 
 PHE   0.008   0.001   PHE C 210 
 TYR   0.018   0.001   TYR A 299 
 ARG   0.003   0.000   ARG A   5 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 1.025 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8389 (t80) cc_final: 0.8156 (t80)
REVERT: B  136 ASP cc_start: 0.8691 (m-30) cc_final: 0.8412 (m-30)
REVERT: C  136 ASP cc_start: 0.8569 (m-30) cc_final: 0.8174 (m-30)
  outliers start: 8
  outliers final: 7
  residues processed: 131
  average time/residue: 0.2185
  time to fit residues: 40.6769
Evaluate side-chains
  127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 120
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain A residue  385 MET
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  323 PHE
Chi-restraints excluded: chain C residue  241 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 86 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0980
   chunk 46 optimal weight:    2.9990
   chunk 88 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.3137 r_free = 0.3137 target = 0.104376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.086457 restraints weight = 12680.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 1.37
r_work: 0.2746 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2617 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2617
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2623
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2623
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10146  Z= 0.162
  Angle     :  0.490   5.798  13626  Z= 0.248
  Chirality :  0.037   0.124   1638
  Planarity :  0.004   0.039   1626
  Dihedral  : 15.253 169.621   1863
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 11.72 %
    Favored  : 87.56 %
  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:  1.78 (0.24), residues: 1248
  helix:  1.66 (0.16), residues: 1041
  sheet:  None (None), residues: 0
  loop : -1.21 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 114 
 PHE   0.008   0.001   PHE C 210 
 TYR   0.018   0.001   TYR C 299 
 ARG   0.004   0.000   ARG A   5 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 120
  time to evaluate  : 0.879 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8350 (t80) cc_final: 0.8098 (t80)
REVERT: B  136 ASP cc_start: 0.8657 (m-30) cc_final: 0.8366 (m-30)
REVERT: C  136 ASP cc_start: 0.8542 (m-30) cc_final: 0.8112 (m-30)
  outliers start: 7
  outliers final: 7
  residues processed: 126
  average time/residue: 0.2224
  time to fit residues: 39.7664
Evaluate side-chains
  124 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain A residue  385 MET
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain C residue  224 VAL
Chi-restraints excluded: chain C residue  241 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 117 optimal weight:    3.9990
   chunk 110 optimal weight:    0.4980
   chunk 37 optimal weight:    0.8980
   chunk 105 optimal weight:    3.9990
   chunk 114 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3106 r_free = 0.3106 target = 0.102253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.084253 restraints weight = 12643.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 1.36
r_work: 0.2717 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2589 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2587
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2587 r_free = 0.2587    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2587 r_free = 0.2587    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2587
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10146  Z= 0.204
  Angle     :  0.514   5.917  13626  Z= 0.260
  Chirality :  0.038   0.122   1638
  Planarity :  0.004   0.039   1626
  Dihedral  : 15.298 168.672   1863
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 11.42 %
    Favored  : 87.87 %
  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:  1.68 (0.24), residues: 1248
  helix:  1.56 (0.16), residues: 1047
  sheet:  None (None), residues: 0
  loop : -1.15 (0.40), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B 114 
 PHE   0.010   0.001   PHE A 323 
 TYR   0.020   0.001   TYR B 299 
 ARG   0.004   0.000   ARG A   5 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 118
  time to evaluate  : 1.114 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8369 (t80) cc_final: 0.8100 (t80)
REVERT: B    5 ARG cc_start: 0.7962 (mtm110) cc_final: 0.7702 (mtm110)
REVERT: B  136 ASP cc_start: 0.8714 (m-30) cc_final: 0.8466 (m-30)
REVERT: C  136 ASP cc_start: 0.8659 (m-30) cc_final: 0.8178 (m-30)
  outliers start: 7
  outliers final: 6
  residues processed: 124
  average time/residue: 0.2341
  time to fit residues: 41.4252
Evaluate side-chains
  121 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain A residue  385 MET
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain C residue  241 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 12 optimal weight:    0.4980
   chunk 38 optimal weight:    0.7980
   chunk 99 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 92 optimal weight:    0.7980
   chunk 71 optimal weight:    0.4980
   chunk 57 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3130 r_free = 0.3130 target = 0.103899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.086001 restraints weight = 12627.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 1.37
r_work: 0.2742 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2615 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2613
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2613 r_free = 0.2613    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2613 r_free = 0.2613    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2613
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10146  Z= 0.164
  Angle     :  0.492   5.827  13626  Z= 0.249
  Chirality :  0.037   0.124   1638
  Planarity :  0.004   0.039   1626
  Dihedral  : 15.024 167.621   1863
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 11.42 %
    Favored  : 87.87 %
  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:  1.81 (0.24), residues: 1248
  helix:  1.66 (0.16), residues: 1044
  sheet:  None (None), residues: 0
  loop : -1.09 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 114 
 PHE   0.008   0.001   PHE C 210 
 TYR   0.018   0.001   TYR C 299 
 ARG   0.005   0.000   ARG A   5 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4377.44 seconds
wall clock time: 78 minutes 25.81 seconds (4705.81 seconds total)