Starting phenix.real_space_refine
on Wed Sep 17 18:03:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x15_21989/09_2025/6x15_21989.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x15_21989/09_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_21989/09_2025/6x15_21989.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x15_21989/09_2025/6x15_21989.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x15_21989/09_2025/6x15_21989.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x15_21989/09_2025/6x15_21989.cif"
  }
  resolution = 3.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.77, per 1000 atoms: 0.28
  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: 1.01
  Conformation dependent library (CDL) restraints added in 386.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.30
  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: 1.58

  Time building geometry restraints manager: 1.30 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: 0.01
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:             1.070
  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:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     10.840
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.650
-------------------------------------------------------------------------------
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= 0.418
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.80 (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
 ARG   0.002   0.000   ARG A 105 
 TYR   0.021   0.002   TYR C 299 
 PHE   0.020   0.002   PHE C 323 
 HIS   0.003   0.001   HIS C 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00863 (10146)
  covalent geometry    : angle       1.25681 (13626)
  hydrogen bonds       : bond        0.13418 (  696)
  hydrogen bonds       : angle       6.30888 ( 2088)

*********************** 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  : 0.305 
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: 0.7770 (m-30)
REVERT: B  267 ASP cc_start: 0.7680 (m-30) cc_final: 0.7465 (m-30)
REVERT: C   22 LEU cc_start: 0.8925 (mt) cc_final: 0.8650 (mt)
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: 0.1215
  time to fit residues: 26.9865
Evaluate side-chains
  116 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9980
   overall best weight:    0.8980

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

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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.103583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.085335 restraints weight = 12160.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 1.33
r_work: 0.2727 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2600 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2600
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2570
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2570 r_free = 0.2570    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2564 r_free = 0.2564    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2564
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10146  Z= 0.131
  Angle     :  0.549   6.465  13626  Z= 0.280
  Chirality :  0.038   0.125   1638
  Planarity :  0.005   0.047   1626
  Dihedral  : 20.873 179.043   1863
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  8.56 %
    Favored  : 90.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.98 (0.22), residues: 1248
  helix: -0.22 (0.15), residues: 1059
  sheet:  None (None), residues: 0
  loop : -2.38 (0.35), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   5 
 TYR   0.026   0.001   TYR B 299 
 PHE   0.013   0.001   PHE A 323 
 HIS   0.003   0.001   HIS B 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (10146)
  covalent geometry    : angle       0.54871 (13626)
  hydrogen bonds       : bond        0.04617 (  696)
  hydrogen bonds       : angle       4.35778 ( 2088)

*********************** 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
  139 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8334 (t80) cc_final: 0.8109 (t80)
REVERT: B   59 MET cc_start: 0.9073 (mmm) cc_final: 0.8857 (mmp)
REVERT: B  136 ASP cc_start: 0.8810 (m-30) cc_final: 0.8556 (m-30)
REVERT: C  136 ASP cc_start: 0.8733 (m-30) cc_final: 0.8160 (m-30)
  outliers start: 8
  outliers final: 5
  residues processed: 136
  average time/residue: 0.0897
  time to fit residues: 17.6764
Evaluate side-chains
  121 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 116
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  385 MET
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 52 optimal weight:    5.9990
   chunk 95 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0030
   chunk 42 optimal weight:    0.6980
   chunk 101 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0570
   chunk 104 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.4708

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.105805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.087545 restraints weight = 12536.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 1.38
r_work: 0.2768 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2641 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2644
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2643 r_free = 0.2643    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2643
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10146  Z= 0.104
  Angle     :  0.498   6.016  13626  Z= 0.250
  Chirality :  0.037   0.124   1638
  Planarity :  0.005   0.043   1626
  Dihedral  : 17.964 174.960   1863
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  9.58 %
    Favored  : 89.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.24), residues: 1248
  helix:  0.59 (0.16), residues: 1056
  sheet:  None (None), residues: 0
  loop : -1.90 (0.37), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   5 
 TYR   0.019   0.001   TYR B 299 
 PHE   0.008   0.001   PHE B  95 
 HIS   0.001   0.000   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 (10146)
  covalent geometry    : angle       0.49777 (13626)
  hydrogen bonds       : bond        0.03726 (  696)
  hydrogen bonds       : angle       4.02600 ( 2088)

*********************** 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
  131 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 125
  time to evaluate  : 0.365 
Fit side-chains
REVERT: B    5 ARG cc_start: 0.7799 (mtm110) cc_final: 0.7528 (mtm110)
REVERT: B   77 ARG cc_start: 0.8503 (ptp-170) cc_final: 0.8206 (ptm160)
REVERT: B  136 ASP cc_start: 0.8679 (m-30) cc_final: 0.8399 (m-30)
REVERT: C   22 LEU cc_start: 0.8810 (mt) cc_final: 0.8457 (mt)
REVERT: C  136 ASP cc_start: 0.8605 (m-30) cc_final: 0.8105 (m-30)
  outliers start: 6
  outliers final: 5
  residues processed: 130
  average time/residue: 0.1027
  time to fit residues: 19.1354
Evaluate side-chains
  130 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 125
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
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  241 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 93 optimal weight:    0.0770
   chunk 70 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 118 optimal weight:    0.8980
   chunk 85 optimal weight:    3.9990
   chunk 117 optimal weight:    0.9990
   overall best weight:    0.6940

-------------------------------------------------------------------------------
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 = 0.3139 r_free = 0.3139 target = 0.104513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.086408 restraints weight = 12595.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 1.37
r_work: 0.2745 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2617 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2617
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2617
|-occupancy refinement: start-------------------------------------------------|
| 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 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2617 r_free = 0.2617    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.2116

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= 0.112
  Angle     :  0.496   5.917  13626  Z= 0.251
  Chirality :  0.037   0.123   1638
  Planarity :  0.004   0.041   1626
  Dihedral  : 17.210 174.153   1863
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.38 %
    Favored  : 89.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.24), residues: 1248
  helix:  0.98 (0.16), residues: 1041
  sheet:  None (None), residues: 0
  loop : -1.64 (0.37), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C   5 
 TYR   0.020   0.001   TYR B 299 
 PHE   0.010   0.001   PHE C  95 
 HIS   0.001   0.000   HIS B 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10146)
  covalent geometry    : angle       0.49574 (13626)
  hydrogen bonds       : bond        0.03834 (  696)
  hydrogen bonds       : angle       3.96002 ( 2088)

*********************** 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
  139 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 0.307 
Fit side-chains
REVERT: B  136 ASP cc_start: 0.8749 (m-30) cc_final: 0.8525 (m-30)
REVERT: B  224 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8112 (m)
REVERT: C  136 ASP cc_start: 0.8679 (m-30) cc_final: 0.8165 (m-30)
  outliers start: 12
  outliers final: 8
  residues processed: 138
  average time/residue: 0.0965
  time to fit residues: 19.1097
Evaluate side-chains
  127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
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  224 VAL
Chi-restraints excluded: chain C residue  241 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 118 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 80 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.104202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.086149 restraints weight = 12590.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 1.37
r_work: 0.2727 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2600 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2600
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2616
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2616 r_free = 0.2616    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2616 r_free = 0.2616    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2616
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10146  Z= 0.111
  Angle     :  0.492   5.911  13626  Z= 0.248
  Chirality :  0.037   0.124   1638
  Planarity :  0.004   0.039   1626
  Dihedral  : 16.443 173.820   1863
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.50 %
    Favored  : 88.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.24), residues: 1248
  helix:  1.35 (0.16), residues: 1029
  sheet:  None (None), residues: 0
  loop : -1.28 (0.38), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A   5 
 TYR   0.020   0.001   TYR C 299 
 PHE   0.009   0.001   PHE A 323 
 HIS   0.002   0.000   HIS B 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (10146)
  covalent geometry    : angle       0.49162 (13626)
  hydrogen bonds       : bond        0.03779 (  696)
  hydrogen bonds       : angle       3.93561 ( 2088)

*********************** 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
  132 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.374 
Fit side-chains
REVERT: B  136 ASP cc_start: 0.8679 (m-30) cc_final: 0.8412 (m-30)
REVERT: B  194 MET cc_start: 0.9405 (mmp) cc_final: 0.9131 (mmp)
REVERT: C  136 ASP cc_start: 0.8599 (m-30) cc_final: 0.8169 (m-30)
  outliers start: 10
  outliers final: 8
  residues processed: 131
  average time/residue: 0.1067
  time to fit residues: 19.9606
Evaluate side-chains
  127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 94 optimal weight:    0.7980
   chunk 95 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   chunk 20 optimal weight:    0.4980
   chunk 87 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 109 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 115 optimal weight:    5.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.103369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.085316 restraints weight = 12740.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 1.38
r_work: 0.2725 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2598 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2576
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2576 r_free = 0.2576    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 = 0.2576 r_free = 0.2576    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2361

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= 0.116
  Angle     :  0.493   5.931  13626  Z= 0.249
  Chirality :  0.038   0.123   1638
  Planarity :  0.004   0.039   1626
  Dihedral  : 16.162 172.833   1863
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 10.81 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.24), residues: 1248
  helix:  1.45 (0.16), residues: 1035
  sheet:  None (None), residues: 0
  loop : -1.36 (0.37), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B   5 
 TYR   0.019   0.001   TYR C 299 
 PHE   0.010   0.001   PHE A 323 
 HIS   0.002   0.000   HIS B 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10146)
  covalent geometry    : angle       0.49310 (13626)
  hydrogen bonds       : bond        0.03915 (  696)
  hydrogen bonds       : angle       3.95958 ( 2088)

*********************** 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
  138 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.369 
Fit side-chains
REVERT: B  136 ASP cc_start: 0.8717 (m-30) cc_final: 0.8477 (m-30)
REVERT: C  136 ASP cc_start: 0.8630 (m-30) cc_final: 0.8171 (m-30)
  outliers start: 13
  outliers final: 9
  residues processed: 136
  average time/residue: 0.1059
  time to fit residues: 20.5283
Evaluate side-chains
  129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
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  224 VAL
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 118 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3118 r_free = 0.3118 target = 0.102963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.084825 restraints weight = 12691.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 1.36
r_work: 0.2722 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2594 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2576
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2576 r_free = 0.2576    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 = 0.2576 r_free = 0.2576    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10146  Z= 0.121
  Angle     :  0.500   5.895  13626  Z= 0.253
  Chirality :  0.038   0.124   1638
  Planarity :  0.004   0.039   1626
  Dihedral  : 16.007 172.399   1863
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.70 %
    Favored  : 88.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.24), residues: 1248
  helix:  1.50 (0.16), residues: 1035
  sheet:  None (None), residues: 0
  loop : -1.30 (0.38), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B   5 
 TYR   0.019   0.001   TYR C 299 
 PHE   0.010   0.001   PHE A 323 
 HIS   0.002   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10146)
  covalent geometry    : angle       0.49988 (13626)
  hydrogen bonds       : bond        0.03991 (  696)
  hydrogen bonds       : angle       3.98568 ( 2088)

*********************** 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
  127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.447 
Fit side-chains
REVERT: B  136 ASP cc_start: 0.8680 (m-30) cc_final: 0.8427 (m-30)
REVERT: C  136 ASP cc_start: 0.8561 (m-30) cc_final: 0.8134 (m-30)
REVERT: C  194 MET cc_start: 0.9435 (mmp) cc_final: 0.8942 (mmt)
  outliers start: 10
  outliers final: 9
  residues processed: 126
  average time/residue: 0.1128
  time to fit residues: 20.0294
Evaluate side-chains
  125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
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  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 106 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0570
   chunk 25 optimal weight:    4.9990
   chunk 111 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 115 optimal weight:    4.9990
   chunk 70 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9990
   chunk 93 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 = 0.3135 r_free = 0.3135 target = 0.104193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.086249 restraints weight = 12649.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.2859 rms_B_bonded: 1.36
r_work: 0.2736 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2609 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2607
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2607 r_free = 0.2607    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 = 0.2607 r_free = 0.2607    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2607
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2486

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= 0.108
  Angle     :  0.483   5.839  13626  Z= 0.245
  Chirality :  0.037   0.124   1638
  Planarity :  0.004   0.039   1626
  Dihedral  : 15.570 171.638   1863
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.01 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.24), residues: 1248
  helix:  1.61 (0.16), residues: 1035
  sheet:  None (None), residues: 0
  loop : -1.18 (0.39), residues: 213

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (10146)
  covalent geometry    : angle       0.48277 (13626)
  hydrogen bonds       : bond        0.03698 (  696)
  hydrogen bonds       : angle       3.93151 ( 2088)

*********************** 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: 11
    poor density    : 121
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8330 (t80) cc_final: 0.8099 (t80)
REVERT: B  136 ASP cc_start: 0.8675 (m-30) cc_final: 0.8411 (m-30)
REVERT: B  194 MET cc_start: 0.9417 (mmp) cc_final: 0.9166 (mmp)
REVERT: C  136 ASP cc_start: 0.8543 (m-30) cc_final: 0.8113 (m-30)
  outliers start: 11
  outliers final: 9
  residues processed: 129
  average time/residue: 0.0996
  time to fit residues: 18.4457
Evaluate side-chains
  127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
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  224 VAL
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 41 optimal weight:    7.9990
   chunk 85 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 113 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3099 r_free = 0.3099 target = 0.101705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.083589 restraints weight = 12659.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.2828 rms_B_bonded: 1.36
r_work: 0.2704 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2576 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2571 r_free = 0.2571    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2571 r_free = 0.2571    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10146  Z= 0.138
  Angle     :  0.518   5.923  13626  Z= 0.262
  Chirality :  0.038   0.123   1638
  Planarity :  0.004   0.039   1626
  Dihedral  : 15.659 171.162   1863
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 11.01 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.24), residues: 1248
  helix:  1.53 (0.16), residues: 1044
  sheet:  None (None), residues: 0
  loop : -1.30 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B   5 
 TYR   0.020   0.001   TYR B 299 
 PHE   0.011   0.001   PHE A 323 
 HIS   0.002   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (10146)
  covalent geometry    : angle       0.51810 (13626)
  hydrogen bonds       : bond        0.04298 (  696)
  hydrogen bonds       : angle       4.03454 ( 2088)

*********************** 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
  123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8323 (t80) cc_final: 0.8049 (t80)
REVERT: B  136 ASP cc_start: 0.8685 (m-30) cc_final: 0.8449 (m-30)
REVERT: C  136 ASP cc_start: 0.8628 (m-30) cc_final: 0.8164 (m-30)
REVERT: C  194 MET cc_start: 0.9445 (mmp) cc_final: 0.9095 (mmt)
  outliers start: 8
  outliers final: 7
  residues processed: 122
  average time/residue: 0.0982
  time to fit residues: 16.9201
Evaluate side-chains
  120 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 33 optimal weight:    0.3980
   chunk 70 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 86 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3127 r_free = 0.3127 target = 0.103703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.085824 restraints weight = 12517.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 1.35
r_work: 0.2728 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2601 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2592
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2592 r_free = 0.2592    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 = 0.2592 r_free = 0.2592    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2592
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.2540

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= 0.111
  Angle     :  0.492   5.860  13626  Z= 0.249
  Chirality :  0.037   0.122   1638
  Planarity :  0.004   0.039   1626
  Dihedral  : 15.254 170.138   1863
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 11.01 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.24), residues: 1248
  helix:  1.64 (0.16), residues: 1044
  sheet:  None (None), residues: 0
  loop : -1.18 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A   5 
 TYR   0.018   0.001   TYR C 299 
 PHE   0.008   0.001   PHE A 323 
 HIS   0.001   0.000   HIS B 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (10146)
  covalent geometry    : angle       0.49153 (13626)
  hydrogen bonds       : bond        0.03788 (  696)
  hydrogen bonds       : angle       3.95197 ( 2088)

********************** 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
  123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8320 (t80) cc_final: 0.8068 (t80)
REVERT: B    5 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7619 (mtm110)
REVERT: B  136 ASP cc_start: 0.8640 (m-30) cc_final: 0.8397 (m-30)
REVERT: B  194 MET cc_start: 0.9430 (mmp) cc_final: 0.9147 (mmp)
REVERT: C  136 ASP cc_start: 0.8542 (m-30) cc_final: 0.8110 (m-30)
  outliers start: 8
  outliers final: 8
  residues processed: 121
  average time/residue: 0.1024
  time to fit residues: 17.6974
Evaluate side-chains
  120 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 119 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 87 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0670
   chunk 63 optimal weight:    0.9980
   chunk 110 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 109 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.6718

-------------------------------------------------------------------------------
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 = 0.103974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.085912 restraints weight = 12678.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.2859 rms_B_bonded: 1.37
r_work: 0.2734 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2606 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2606
-------------------------------------------------------------------------------
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 = 0.06   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: 0.8594
moved from start:          0.2595

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= 0.110
  Angle     :  0.490   5.828  13626  Z= 0.248
  Chirality :  0.037   0.124   1638
  Planarity :  0.004   0.039   1626
  Dihedral  : 14.991 168.699   1863
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 11.11 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.24), residues: 1248
  helix:  1.66 (0.16), residues: 1047
  sheet:  None (None), residues: 0
  loop : -1.05 (0.41), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   5 
 TYR   0.018   0.001   TYR C 299 
 PHE   0.008   0.001   PHE A 323 
 HIS   0.001   0.000   HIS B 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (10146)
  covalent geometry    : angle       0.49028 (13626)
  hydrogen bonds       : bond        0.03769 (  696)
  hydrogen bonds       : angle       3.93173 ( 2088)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2252.21 seconds
wall clock time: 39 minutes 21.40 seconds (2361.40 seconds total)