Starting phenix.real_space_refine
on Wed Sep 17 09:44:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6kng_0731/09_2025/6kng_0731.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6kng_0731/09_2025/6kng_0731.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6kng_0731/09_2025/6kng_0731.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6kng_0731/09_2025/6kng_0731.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6kng_0731/09_2025/6kng_0731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6kng_0731/09_2025/6kng_0731.map"
  }
  resolution = 2.85
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Cu      6      5.60       5
     S      30      5.16       5
     C    4935      2.51       5
     N    1326      2.21       5
     O    1452      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: 7749
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2581
          Classifications: {'peptide': 334}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 311}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CU': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1005  SG  CYS A 136      24.373  25.147  33.465  1.00 55.95           S

  Restraints were copied for chains:
    B, C
  Time building chain proxies: 1.74, per 1000 atoms: 0.22
  Number of scatterers: 7749
  At special positions: 0
  Unit cell: (92.4, 93.28, 77.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cu      6     28.99
     S      30     16.00
     O    1452      8.00
     N    1326      7.00
     C    4935      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 387.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1806

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 18 sheets defined
      12.9% alpha, 40.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 12
      removed outlier: 3.945A  pdb=" N   THR A  11 " --> pdb=" O   ASP A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 109
    Processing helix  chain 'A' and resid 141 through 147
    Processing helix  chain 'A' and resid 198 through 211
      removed outlier: 3.678A  pdb=" N   ALA A 202 " --> pdb=" O   THR A 198 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   GLU A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   ASP A 205 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 4.076A  pdb=" N   HIS A 231 " --> pdb=" O   THR A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 313
    Processing helix  chain 'B' and resid 8 through 12
      removed outlier: 3.944A  pdb=" N   THR B  11 " --> pdb=" O   ASP B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 109
    Processing helix  chain 'B' and resid 141 through 147
    Processing helix  chain 'B' and resid 198 through 211
      removed outlier: 3.678A  pdb=" N   ALA B 202 " --> pdb=" O   THR B 198 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   GLU B 204 " --> pdb=" O   GLY B 200 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   ASP B 205 " --> pdb=" O   GLU B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 232
      removed outlier: 4.075A  pdb=" N   HIS B 231 " --> pdb=" O   THR B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 313
    Processing helix  chain 'C' and resid 8 through 12
      removed outlier: 3.945A  pdb=" N   THR C  11 " --> pdb=" O   ASP C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 109
    Processing helix  chain 'C' and resid 141 through 147
    Processing helix  chain 'C' and resid 198 through 211
      removed outlier: 3.679A  pdb=" N   ALA C 202 " --> pdb=" O   THR C 198 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   GLU C 204 " --> pdb=" O   GLY C 200 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   ASP C 205 " --> pdb=" O   GLU C 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 232
      removed outlier: 4.076A  pdb=" N   HIS C 231 " --> pdb=" O   THR C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 313
    Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16
      removed outlier: 6.899A  pdb=" N   VAL A  15 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
      removed outlier: 8.810A  pdb=" N   THR A  42 " --> pdb=" O   VAL A  15 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16
      removed outlier: 6.899A  pdb=" N   VAL A  15 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
      removed outlier: 8.810A  pdb=" N   THR A  42 " --> pdb=" O   VAL A  15 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   VAL A  39 " --> pdb=" O   GLU A  82 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   ARG A  84 " --> pdb=" O   VAL A  39 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   PHE A  41 " --> pdb=" O   ARG A  84 " (cutoff:3.500A)
      removed outlier: 8.275A  pdb=" N   ILE A  86 " --> pdb=" O   PHE A  41 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   MET A  43 " --> pdb=" O   ILE A  86 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   THR A 121 " --> pdb=" O   LYS C 336 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   LYS C 336 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   ARG A 123 " --> pdb=" O   VAL C 334 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   VAL C 334 " --> pdb=" O   ARG A 123 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   LYS A 125 " --> pdb=" O   THR C 332 " (cutoff:3.500A)
      removed outlier: 9.136A  pdb=" N   THR C 332 " --> pdb=" O   LYS A 125 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76
      removed outlier: 6.517A  pdb=" N   MET A  73 " --> pdb=" O   MET A 155 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   LEU A 157 " --> pdb=" O   MET A  73 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   VAL A  75 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 163
      removed outlier: 4.215A  pdb=" N   LEU A 162 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 217 through 220
      removed outlier: 6.727A  pdb=" N   LYS A 174 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   VAL A 244 " --> pdb=" O   LYS A 174 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   TYR A 176 " --> pdb=" O   VAL A 244 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   SER A 246 " --> pdb=" O   TYR A 176 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   VAL A 178 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
      removed outlier: 8.190A  pdb=" N   THR A 294 " --> pdb=" O   GLY A 261 " (cutoff:3.500A)
      removed outlier: 8.537A  pdb=" N   GLY A 261 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ASP A 262 " --> pdb=" O   ASP A 277 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ASP A 277 " --> pdb=" O   ASP A 262 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 233 through 236
      removed outlier: 3.960A  pdb=" N   ALA A 302 " --> pdb=" O   ILE A 257 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 331 through 338
      removed outlier: 9.133A  pdb=" N   THR A 332 " --> pdb=" O   LYS B 125 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   LYS B 125 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   VAL A 334 " --> pdb=" O   ARG B 123 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   ARG B 123 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   LYS A 336 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   THR B 121 " --> pdb=" O   LYS A 336 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   VAL B  39 " --> pdb=" O   GLU B  82 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ARG B  84 " --> pdb=" O   VAL B  39 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   PHE B  41 " --> pdb=" O   ARG B  84 " (cutoff:3.500A)
      removed outlier: 8.275A  pdb=" N   ILE B  86 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   MET B  43 " --> pdb=" O   ILE B  86 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   VAL B  15 " --> pdb=" O   GLU B  40 " (cutoff:3.500A)
      removed outlier: 8.811A  pdb=" N   THR B  42 " --> pdb=" O   VAL B  15 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 331 through 338
      removed outlier: 9.133A  pdb=" N   THR A 332 " --> pdb=" O   LYS B 125 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   LYS B 125 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   VAL A 334 " --> pdb=" O   ARG B 123 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   ARG B 123 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   LYS A 336 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   THR B 121 " --> pdb=" O   LYS A 336 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   VAL B  39 " --> pdb=" O   GLU B  82 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ARG B  84 " --> pdb=" O   VAL B  39 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   PHE B  41 " --> pdb=" O   ARG B  84 " (cutoff:3.500A)
      removed outlier: 8.275A  pdb=" N   ILE B  86 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   MET B  43 " --> pdb=" O   ILE B  86 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 73 through 76
      removed outlier: 6.519A  pdb=" N   MET B  73 " --> pdb=" O   MET B 155 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   LEU B 157 " --> pdb=" O   MET B  73 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   VAL B  75 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 162 through 163
      removed outlier: 4.216A  pdb=" N   LEU B 162 " --> pdb=" O   LEU B 170 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 217 through 220
      removed outlier: 6.726A  pdb=" N   LYS B 174 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   VAL B 244 " --> pdb=" O   LYS B 174 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   TYR B 176 " --> pdb=" O   VAL B 244 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   SER B 246 " --> pdb=" O   TYR B 176 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   VAL B 178 " --> pdb=" O   SER B 246 " (cutoff:3.500A)
      removed outlier: 8.189A  pdb=" N   THR B 294 " --> pdb=" O   GLY B 261 " (cutoff:3.500A)
      removed outlier: 8.536A  pdb=" N   GLY B 261 " --> pdb=" O   THR B 294 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   ASP B 262 " --> pdb=" O   ASP B 277 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ASP B 277 " --> pdb=" O   ASP B 262 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 233 through 236
      removed outlier: 3.962A  pdb=" N   ALA B 302 " --> pdb=" O   ILE B 257 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 331 through 338
      removed outlier: 9.112A  pdb=" N   THR B 332 " --> pdb=" O   LYS C 125 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   LYS C 125 " --> pdb=" O   THR B 332 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   VAL B 334 " --> pdb=" O   ARG C 123 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   ARG C 123 " --> pdb=" O   VAL B 334 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   LYS B 336 " --> pdb=" O   THR C 121 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   THR C 121 " --> pdb=" O   LYS B 336 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   VAL C  39 " --> pdb=" O   GLU C  82 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ARG C  84 " --> pdb=" O   VAL C  39 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   PHE C  41 " --> pdb=" O   ARG C  84 " (cutoff:3.500A)
      removed outlier: 8.276A  pdb=" N   ILE C  86 " --> pdb=" O   PHE C  41 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   MET C  43 " --> pdb=" O   ILE C  86 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   VAL C  15 " --> pdb=" O   GLU C  40 " (cutoff:3.500A)
      removed outlier: 8.811A  pdb=" N   THR C  42 " --> pdb=" O   VAL C  15 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 331 through 338
      removed outlier: 9.112A  pdb=" N   THR B 332 " --> pdb=" O   LYS C 125 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   LYS C 125 " --> pdb=" O   THR B 332 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   VAL B 334 " --> pdb=" O   ARG C 123 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   ARG C 123 " --> pdb=" O   VAL B 334 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   LYS B 336 " --> pdb=" O   THR C 121 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   THR C 121 " --> pdb=" O   LYS B 336 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   VAL C  39 " --> pdb=" O   GLU C  82 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ARG C  84 " --> pdb=" O   VAL C  39 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   PHE C  41 " --> pdb=" O   ARG C  84 " (cutoff:3.500A)
      removed outlier: 8.276A  pdb=" N   ILE C  86 " --> pdb=" O   PHE C  41 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   MET C  43 " --> pdb=" O   ILE C  86 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 73 through 76
      removed outlier: 6.517A  pdb=" N   MET C  73 " --> pdb=" O   MET C 155 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   LEU C 157 " --> pdb=" O   MET C  73 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   VAL C  75 " --> pdb=" O   LEU C 157 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 162 through 163
      removed outlier: 4.216A  pdb=" N   LEU C 162 " --> pdb=" O   LEU C 170 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 217 through 220
      removed outlier: 6.726A  pdb=" N   LYS C 174 " --> pdb=" O   LEU C 242 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   VAL C 244 " --> pdb=" O   LYS C 174 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   TYR C 176 " --> pdb=" O   VAL C 244 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   SER C 246 " --> pdb=" O   TYR C 176 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   VAL C 178 " --> pdb=" O   SER C 246 " (cutoff:3.500A)
      removed outlier: 8.189A  pdb=" N   THR C 294 " --> pdb=" O   GLY C 261 " (cutoff:3.500A)
      removed outlier: 8.537A  pdb=" N   GLY C 261 " --> pdb=" O   THR C 294 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ASP C 262 " --> pdb=" O   ASP C 277 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ASP C 277 " --> pdb=" O   ASP C 262 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 233 through 236
      removed outlier: 3.960A  pdb=" N   ALA C 302 " --> pdb=" O   ILE C 257 " (cutoff:3.500A)

    233 hydrogen bonds defined for protein.
    594 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: 1.03

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2554
        1.34 -     1.45: 1241
        1.45 -     1.57: 4101
        1.57 -     1.69: 0
        1.69 -     1.81: 57
  Bond restraints: 7953
  Sorted by residual:
  bond pdb=" CB  ILE B   9 "
       pdb=" CG1 ILE B   9 "
    ideal  model  delta    sigma   weight residual
    1.530  1.559 -0.029 2.00e-02 2.50e+03 2.12e+00
  bond pdb=" CB  ILE A   9 "
       pdb=" CG1 ILE A   9 "
    ideal  model  delta    sigma   weight residual
    1.530  1.559 -0.029 2.00e-02 2.50e+03 2.10e+00
  bond pdb=" CB  ILE C   9 "
       pdb=" CG1 ILE C   9 "
    ideal  model  delta    sigma   weight residual
    1.530  1.559 -0.029 2.00e-02 2.50e+03 2.05e+00
  bond pdb=" CG  LYS C 166 "
       pdb=" CD  LYS C 166 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.79e-01
  bond pdb=" CG  LYS B 166 "
       pdb=" CD  LYS B 166 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.28e-01
  ... (remaining 7948 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 10690
        2.10 -     4.21: 127
        4.21 -     6.31: 10
        6.31 -     8.42: 12
        8.42 -    10.52: 6
  Bond angle restraints: 10845
  Sorted by residual:
  angle pdb=" CA  ILE B   9 "
        pdb=" CB  ILE B   9 "
        pdb=" CG1 ILE B   9 "
      ideal   model   delta    sigma   weight residual
     110.40  119.20   -8.80 1.70e+00 3.46e-01 2.68e+01
  angle pdb=" CA  ILE C   9 "
        pdb=" CB  ILE C   9 "
        pdb=" CG1 ILE C   9 "
      ideal   model   delta    sigma   weight residual
     110.40  119.19   -8.79 1.70e+00 3.46e-01 2.67e+01
  angle pdb=" CA  ILE A   9 "
        pdb=" CB  ILE A   9 "
        pdb=" CG1 ILE A   9 "
      ideal   model   delta    sigma   weight residual
     110.40  119.18   -8.78 1.70e+00 3.46e-01 2.67e+01
  angle pdb=" CB  ILE A   9 "
        pdb=" CG1 ILE A   9 "
        pdb=" CD1 ILE A   9 "
      ideal   model   delta    sigma   weight residual
     113.80  124.32  -10.52 2.10e+00 2.27e-01 2.51e+01
  angle pdb=" CB  ILE C   9 "
        pdb=" CG1 ILE C   9 "
        pdb=" CD1 ILE C   9 "
      ideal   model   delta    sigma   weight residual
     113.80  124.31  -10.51 2.10e+00 2.27e-01 2.50e+01
  ... (remaining 10840 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.73: 4205
       16.73 -    33.45: 328
       33.45 -    50.18: 81
       50.18 -    66.90: 33
       66.90 -    83.63: 9
  Dihedral angle restraints: 4656
    sinusoidal: 1812
      harmonic: 2844
  Sorted by residual:
  dihedral pdb=" CA  HIS C 306 "
           pdb=" C   HIS C 306 "
           pdb=" N   ASN C 307 "
           pdb=" CA  ASN C 307 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.85   26.15     0      5.00e+00 4.00e-02 2.74e+01
  dihedral pdb=" CA  HIS A 306 "
           pdb=" C   HIS A 306 "
           pdb=" N   ASN A 307 "
           pdb=" CA  ASN A 307 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.88   26.12     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" CA  HIS B 306 "
           pdb=" C   HIS B 306 "
           pdb=" N   ASN B 307 "
           pdb=" CA  ASN B 307 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.92   26.08     0      5.00e+00 4.00e-02 2.72e+01
  ... (remaining 4653 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 690
       0.032 -    0.063: 289
       0.063 -    0.094: 142
       0.094 -    0.126: 65
       0.126 -    0.157: 11
  Chirality restraints: 1197
  Sorted by residual:
  chirality pdb=" CB  ILE A   9 "
            pdb=" CA  ILE A   9 "
            pdb=" CG1 ILE A   9 "
            pdb=" CG2 ILE A   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.20e-01
  chirality pdb=" CB  ILE B   9 "
            pdb=" CA  ILE B   9 "
            pdb=" CG1 ILE B   9 "
            pdb=" CG2 ILE B   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.06e-01
  chirality pdb=" CB  ILE C   9 "
            pdb=" CA  ILE C   9 "
            pdb=" CG1 ILE C   9 "
            pdb=" CG2 ILE C   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.70e-01
  ... (remaining 1194 not shown)

  Planarity restraints: 1422
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 198 "    0.020 5.00e-02 4.00e+02   3.05e-02 1.49e+00
        pdb=" N   PRO A 199 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 199 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 199 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 198 "   -0.020 5.00e-02 4.00e+02   3.04e-02 1.48e+00
        pdb=" N   PRO C 199 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO C 199 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 199 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 115 "   -0.020 5.00e-02 4.00e+02   3.04e-02 1.47e+00
        pdb=" N   PRO C 116 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO C 116 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 116 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1419 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 134
        2.65 -     3.22: 6625
        3.22 -     3.78: 11078
        3.78 -     4.34: 16985
        4.34 -     4.90: 28331
  Nonbonded interactions: 63153
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS C 306 "
            pdb="CU    CU A 501 "
     model   vdw
     2.093 2.320
  nonbonded pdb=" NE2 HIS A 100 "
            pdb="CU    CU A 501 "
     model   vdw
     2.113 2.320
  nonbonded pdb=" NE2 HIS B 100 "
            pdb="CU    CU B 501 "
     model   vdw
     2.114 2.320
  nonbonded pdb=" NE2 HIS C 100 "
            pdb="CU    CU C 501 "
     model   vdw
     2.114 2.320
  nonbonded pdb=" NE2 HIS B 306 "
            pdb="CU    CU C 501 "
     model   vdw
     2.115 2.320
  ... (remaining 63148 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 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:             9.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.800
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8808
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      :  0.005   0.036   7953  Z= 0.199
  Angle     :  0.653  10.523  10845  Z= 0.353
  Chirality :  0.048   0.157   1197
  Planarity :  0.004   0.031   1422
  Dihedral  : 14.335  83.626   2850
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 11.03 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -2.31 (0.21), residues: 996
  helix: -2.51 (0.47), residues: 69
  sheet: -0.28 (0.28), residues: 282
  loop : -2.13 (0.18), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 123 
 TYR   0.010   0.001   TYR A 134 
 PHE   0.012   0.002   PHE C 320 
 TRP   0.004   0.001   TRP B 265 
 HIS   0.006   0.001   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 7953)
  covalent geometry    : angle       0.65328 (10845)
  hydrogen bonds       : bond        0.11969 (  213)
  hydrogen bonds       : angle       6.66258 (  594)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 78
  time to evaluate  : 0.311 
Fit side-chains
REVERT: B   30 GLN cc_start: 0.8709 (mt0) cc_final: 0.8457 (mt0)
REVERT: C  231 HIS cc_start: 0.8170 (m90) cc_final: 0.7866 (m-70)
  outliers start: 30
  outliers final: 5
  residues processed: 102
  average time/residue: 0.6154
  time to fit residues: 66.1808
Evaluate side-chains
  60 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain B residue  313 GLU
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue  313 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    0.0870
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0570
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.3876

-------------------------------------------------------------------------------
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 = 0.3115 r_free = 0.3115 target = 0.091368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.074117 restraints weight = 11788.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 2.24
r_work: 0.2714 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2578 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8964
moved from start:          0.1035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7953  Z= 0.110
  Angle     :  0.492   5.347  10845  Z= 0.261
  Chirality :  0.045   0.126   1197
  Planarity :  0.004   0.029   1422
  Dihedral  :  5.692  44.911   1085
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 14.58 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.45 (0.23), residues: 996
  helix: -1.61 (0.57), residues: 69
  sheet:  0.34 (0.29), residues: 261
  loop : -1.52 (0.20), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 159 
 TYR   0.008   0.001   TYR B 134 
 PHE   0.009   0.001   PHE C 320 
 TRP   0.005   0.001   TRP C 265 
 HIS   0.005   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7953)
  covalent geometry    : angle       0.49212 (10845)
  hydrogen bonds       : bond        0.03326 (  213)
  hydrogen bonds       : angle       5.78865 (  594)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 64
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8468 (mt0)
REVERT: B  113 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8447 (mt0)
REVERT: C  113 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8470 (mt0)
REVERT: C  165 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7873 (pm20)
REVERT: C  231 HIS cc_start: 0.8476 (m90) cc_final: 0.8203 (m-70)
  outliers start: 23
  outliers final: 5
  residues processed: 79
  average time/residue: 0.5473
  time to fit residues: 45.8369
Evaluate side-chains
  64 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue  113 GLN
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  165 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 2 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
B  60 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.089679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.072056 restraints weight = 11769.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.2801 rms_B_bonded: 2.24
r_work: 0.2678 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2542 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8980
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7953  Z= 0.198
  Angle     :  0.540   5.583  10845  Z= 0.289
  Chirality :  0.047   0.147   1197
  Planarity :  0.004   0.030   1422
  Dihedral  :  4.887  27.714   1075
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 13.85 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.14 (0.23), residues: 996
  helix: -1.24 (0.60), residues: 69
  sheet:  0.47 (0.29), residues: 270
  loop : -1.31 (0.21), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  84 
 TYR   0.013   0.001   TYR B 134 
 PHE   0.012   0.002   PHE A 320 
 TRP   0.005   0.001   TRP C 265 
 HIS   0.006   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 ( 7953)
  covalent geometry    : angle       0.53989 (10845)
  hydrogen bonds       : bond        0.04120 (  213)
  hydrogen bonds       : angle       5.83218 (  594)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 53
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8476 (mt0)
REVERT: B  113 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8484 (mt0)
REVERT: B  165 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7790 (pm20)
REVERT: C  113 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8522 (mt0)
REVERT: C  165 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7909 (pm20)
REVERT: C  231 HIS cc_start: 0.8516 (m90) cc_final: 0.8304 (m-70)
  outliers start: 31
  outliers final: 13
  residues processed: 75
  average time/residue: 0.5662
  time to fit residues: 45.1620
Evaluate side-chains
  69 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 51
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  113 GLN
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue    9 ILE
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  165 GLU
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  165 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0670
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 94 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 97 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.9522

-------------------------------------------------------------------------------
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 = 0.3086 r_free = 0.3086 target = 0.089498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.072078 restraints weight = 11923.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.2800 rms_B_bonded: 2.21
r_work: 0.2680 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2546 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8992
moved from start:          0.1321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7953  Z= 0.193
  Angle     :  0.538   5.598  10845  Z= 0.289
  Chirality :  0.047   0.145   1197
  Planarity :  0.004   0.034   1422
  Dihedral  :  4.879  27.958   1075
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 13.48 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.91 (0.24), residues: 996
  helix: -1.06 (0.60), residues: 69
  sheet:  0.68 (0.29), residues: 270
  loop : -1.17 (0.21), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  84 
 TYR   0.013   0.001   TYR B 134 
 PHE   0.012   0.002   PHE C 320 
 TRP   0.005   0.001   TRP C 265 
 HIS   0.006   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 7953)
  covalent geometry    : angle       0.53822 (10845)
  hydrogen bonds       : bond        0.04029 (  213)
  hydrogen bonds       : angle       5.78892 (  594)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 55
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8624 (mm-40)
REVERT: B  113 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8472 (mt0)
REVERT: B  165 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7781 (pm20)
REVERT: C  113 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8525 (mt0)
REVERT: C  165 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7966 (pm20)
REVERT: C  231 HIS cc_start: 0.8541 (m90) cc_final: 0.8331 (m-70)
  outliers start: 37
  outliers final: 18
  residues processed: 85
  average time/residue: 0.5417
  time to fit residues: 48.9104
Evaluate side-chains
  74 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 51
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   43 MET
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  113 GLN
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  165 GLU
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  253 ARG
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  165 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 98 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.3072 r_free = 0.3072 target = 0.088682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.071111 restraints weight = 11853.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.2786 rms_B_bonded: 2.25
r_work: 0.2663 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2526 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8990
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   7953  Z= 0.236
  Angle     :  0.566   5.889  10845  Z= 0.304
  Chirality :  0.049   0.156   1197
  Planarity :  0.004   0.035   1422
  Dihedral  :  5.023  28.698   1075
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 14.46 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.86 (0.24), residues: 996
  helix: -0.97 (0.60), residues: 69
  sheet:  0.72 (0.29), residues: 270
  loop : -1.15 (0.21), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  84 
 TYR   0.014   0.001   TYR B 134 
 PHE   0.013   0.002   PHE A 292 
 TRP   0.006   0.001   TRP C 265 
 HIS   0.006   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 ( 7953)
  covalent geometry    : angle       0.56551 (10845)
  hydrogen bonds       : bond        0.04370 (  213)
  hydrogen bonds       : angle       5.80936 (  594)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 53
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8676 (mm-40)
REVERT: B  113 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8482 (mt0)
REVERT: B  165 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.7866 (pm20)
REVERT: C   43 MET cc_start: 0.9386 (mtm) cc_final: 0.9143 (mtm)
REVERT: C  113 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8571 (mt0)
REVERT: C  165 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8071 (pm20)
  outliers start: 31
  outliers final: 17
  residues processed: 76
  average time/residue: 0.5501
  time to fit residues: 44.3990
Evaluate side-chains
  71 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 49
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   43 MET
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  113 GLN
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  165 GLU
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  253 ARG
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  165 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 51 optimal weight:    0.3980
   chunk 18 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  60 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.089210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.071850 restraints weight = 11882.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.2797 rms_B_bonded: 2.21
r_work: 0.2676 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2539 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8994
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   7953  Z= 0.195
  Angle     :  0.542   5.599  10845  Z= 0.291
  Chirality :  0.047   0.146   1197
  Planarity :  0.004   0.036   1422
  Dihedral  :  4.903  27.852   1075
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 15.44 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.69 (0.24), residues: 996
  helix: -0.87 (0.60), residues: 69
  sheet:  1.00 (0.29), residues: 264
  loop : -1.09 (0.21), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  84 
 TYR   0.012   0.001   TYR B 134 
 PHE   0.013   0.002   PHE C 320 
 TRP   0.006   0.001   TRP C 265 
 HIS   0.006   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 7953)
  covalent geometry    : angle       0.54196 (10845)
  hydrogen bonds       : bond        0.04047 (  213)
  hydrogen bonds       : angle       5.70137 (  594)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 54
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8663 (mm-40)
REVERT: B  113 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8470 (mt0)
REVERT: B  165 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.7860 (pm20)
REVERT: C  113 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8533 (mt0)
REVERT: C  165 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8063 (pm20)
  outliers start: 34
  outliers final: 19
  residues processed: 79
  average time/residue: 0.5396
  time to fit residues: 45.2241
Evaluate side-chains
  73 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 49
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   43 MET
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  113 GLN
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  165 GLU
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  253 ARG
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  165 GLU
Chi-restraints excluded: chain C residue  228 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 1 optimal weight:    0.3980
   chunk 80 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   chunk 85 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3094 r_free = 0.3094 target = 0.090166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.072859 restraints weight = 11743.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 2.20
r_work: 0.2691 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2554 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8981
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7953  Z= 0.159
  Angle     :  0.523   5.537  10845  Z= 0.280
  Chirality :  0.046   0.137   1197
  Planarity :  0.004   0.036   1422
  Dihedral  :  4.767  27.312   1075
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 16.30 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.56 (0.24), residues: 996
  helix: -0.74 (0.60), residues: 69
  sheet:  1.14 (0.30), residues: 264
  loop : -1.03 (0.22), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  37 
 TYR   0.011   0.001   TYR A 134 
 PHE   0.012   0.002   PHE C 320 
 TRP   0.006   0.001   TRP C 265 
 HIS   0.005   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 7953)
  covalent geometry    : angle       0.52322 (10845)
  hydrogen bonds       : bond        0.03766 (  213)
  hydrogen bonds       : angle       5.53477 (  594)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 52
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8643 (mm-40)
REVERT: B  113 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8478 (mt0)
REVERT: C  113 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8530 (mt0)
REVERT: C  165 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8025 (pm20)
  outliers start: 31
  outliers final: 19
  residues processed: 77
  average time/residue: 0.6466
  time to fit residues: 52.5311
Evaluate side-chains
  73 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 50
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   43 MET
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  113 GLN
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  253 ARG
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  165 GLU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  253 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 76 optimal weight:    0.4980
   chunk 53 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   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 = 0.3093 r_free = 0.3093 target = 0.090003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.072569 restraints weight = 11856.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.2810 rms_B_bonded: 2.22
r_work: 0.2689 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2553 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8982
moved from start:          0.1550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7953  Z= 0.166
  Angle     :  0.535   7.778  10845  Z= 0.284
  Chirality :  0.047   0.140   1197
  Planarity :  0.004   0.036   1422
  Dihedral  :  4.773  27.627   1075
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 16.42 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.54 (0.24), residues: 996
  helix: -0.65 (0.60), residues: 69
  sheet:  1.02 (0.29), residues: 270
  loop : -0.98 (0.22), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  84 
 TYR   0.011   0.001   TYR B 134 
 PHE   0.012   0.002   PHE C 320 
 TRP   0.006   0.001   TRP C 265 
 HIS   0.005   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 7953)
  covalent geometry    : angle       0.53476 (10845)
  hydrogen bonds       : bond        0.03805 (  213)
  hydrogen bonds       : angle       5.49918 (  594)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 53
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8633 (mm-40)
REVERT: B  113 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8472 (mt0)
REVERT: C  113 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8532 (mt0)
REVERT: C  165 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8045 (pm20)
  outliers start: 30
  outliers final: 19
  residues processed: 77
  average time/residue: 0.6263
  time to fit residues: 50.8886
Evaluate side-chains
  74 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 51
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  113 GLN
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  253 ARG
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  165 GLU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  253 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 81 optimal weight:    0.0970
   chunk 56 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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 = 0.3066 r_free = 0.3066 target = 0.088291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.070850 restraints weight = 11840.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.2779 rms_B_bonded: 2.22
r_work: 0.2657 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2522 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9009
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   7953  Z= 0.275
  Angle     :  0.601   7.545  10845  Z= 0.321
  Chirality :  0.050   0.165   1197
  Planarity :  0.004   0.037   1422
  Dihedral  :  5.122  29.513   1075
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 16.05 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.70 (0.24), residues: 996
  helix: -0.82 (0.60), residues: 69
  sheet:  0.89 (0.29), residues: 270
  loop : -1.08 (0.22), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  84 
 TYR   0.016   0.002   TYR B 134 
 PHE   0.015   0.002   PHE B 292 
 TRP   0.006   0.001   TRP C 265 
 HIS   0.007   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00661 ( 7953)
  covalent geometry    : angle       0.60109 (10845)
  hydrogen bonds       : bond        0.04626 (  213)
  hydrogen bonds       : angle       5.75026 (  594)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 51
  time to evaluate  : 0.321 
Fit side-chains
REVERT: B  113 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8460 (mt0)
REVERT: C  113 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8548 (mt0)
REVERT: C  165 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8114 (pm20)
  outliers start: 30
  outliers final: 19
  residues processed: 74
  average time/residue: 0.5938
  time to fit residues: 46.6267
Evaluate side-chains
  70 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 48
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  253 ARG
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  165 GLU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  253 ARG
Chi-restraints excluded: chain C residue  340 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 33 optimal weight:    0.2980
   chunk 7 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0020
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.4388

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

Flipped N/Q/H residues before XYZ refinement:
A  76 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.092307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.075009 restraints weight = 11374.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 2.22
r_work: 0.2733 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2599 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8950
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7953  Z= 0.118
  Angle     :  0.507   5.464  10845  Z= 0.269
  Chirality :  0.045   0.126   1197
  Planarity :  0.004   0.036   1422
  Dihedral  :  4.596  25.947   1075
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.65 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.38 (0.24), residues: 996
  helix: -0.68 (0.59), residues: 72
  sheet:  1.25 (0.29), residues: 264
  loop : -0.89 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 159 
 TYR   0.008   0.001   TYR B 134 
 PHE   0.011   0.001   PHE B 320 
 TRP   0.006   0.001   TRP C 265 
 HIS   0.004   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7953)
  covalent geometry    : angle       0.50700 (10845)
  hydrogen bonds       : bond        0.03331 (  213)
  hydrogen bonds       : angle       5.36334 (  594)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 52
  time to evaluate  : 0.321 
Fit side-chains
REVERT: B  113 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8505 (mt0)
REVERT: C  113 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8546 (mt0)
REVERT: C  165 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7842 (pm20)
  outliers start: 19
  outliers final: 11
  residues processed: 68
  average time/residue: 0.6788
  time to fit residues: 48.8640
Evaluate side-chains
  65 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  253 ARG
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  165 GLU
Chi-restraints excluded: chain C residue  253 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0770
   chunk 45 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0570
   overall best weight:    0.4056

-------------------------------------------------------------------------------
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 = 0.3138 r_free = 0.3138 target = 0.092669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.075416 restraints weight = 11356.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 2.21
r_work: 0.2742 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2605 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8940
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7953  Z= 0.111
  Angle     :  0.502   9.084  10845  Z= 0.265
  Chirality :  0.045   0.129   1197
  Planarity :  0.004   0.036   1422
  Dihedral  :  4.480  25.294   1075
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 18.38 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.23 (0.24), residues: 996
  helix: -0.58 (0.59), residues: 72
  sheet:  1.41 (0.29), residues: 261
  loop : -0.79 (0.22), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 253 
 TYR   0.007   0.001   TYR B 134 
 PHE   0.011   0.001   PHE B 320 
 TRP   0.005   0.001   TRP A 265 
 HIS   0.004   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7953)
  covalent geometry    : angle       0.50209 (10845)
  hydrogen bonds       : bond        0.03248 (  213)
  hydrogen bonds       : angle       5.20939 (  594)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2352.39 seconds
wall clock time: 40 minutes 57.60 seconds (2457.60 seconds total)