Starting phenix.real_space_refine
on Wed Feb 12 11:04:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6kng_0731/02_2025/6kng_0731.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6kng_0731/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6kng_0731/02_2025/6kng_0731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6kng_0731/02_2025/6kng_0731.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6kng_0731/02_2025/6kng_0731.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6kng_0731/02_2025/6kng_0731.cif"
  }
  resolution = 2.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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:
    C, B
  Time building chain proxies: 2.99, per 1000 atoms: 0.39
  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: 1.74
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.01
  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: 2.21

  Time building geometry restraints manager: 2.00 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             24.820
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     16.350
  Find NCS groups from input model:        0.140
  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:12.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.580
-------------------------------------------------------------------------------
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= 0.304
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.004   0.001   TRP B 265 
 HIS   0.006   0.001   HIS B 306 
 PHE   0.012   0.002   PHE C 320 
 TYR   0.010   0.001   TYR A 134 
 ARG   0.002   0.000   ARG A 123 

*********************** 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  : 0.904 
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: 1.4087
  time to fit residues: 151.5194
Evaluate side-chains
  61 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
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 83 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3068 r_free = 0.3068 target = 0.088295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.071070 restraints weight = 11808.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.2782 rms_B_bonded: 2.20
r_work: 0.2660 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2524 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9011
moved from start:          0.1071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   7953  Z= 0.404
  Angle     :  0.580   5.675  10845  Z= 0.311
  Chirality :  0.049   0.152   1197
  Planarity :  0.004   0.029   1422
  Dihedral  :  6.052  42.078   1085
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 13.48 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.23), residues: 996
  helix: -1.68 (0.55), residues: 69
  sheet:  0.02 (0.28), residues: 288
  loop : -1.55 (0.20), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 265 
 HIS   0.007   0.001   HIS C 306 
 PHE   0.013   0.002   PHE B 292 
 TYR   0.015   0.002   TYR B 134 
 ARG   0.002   0.001   ARG C 159 

*********************** 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
  83 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 56
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8457 (mt0)
REVERT: B  113 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8463 (mt0)
REVERT: C  113 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8460 (mt0)
REVERT: C  165 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8031 (pm20)
REVERT: C  231 HIS cc_start: 0.8509 (m90) cc_final: 0.8264 (m-70)
  outliers start: 27
  outliers final: 13
  residues processed: 75
  average time/residue: 1.2318
  time to fit residues: 98.4483
Evaluate side-chains
  70 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
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  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  287 THR
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
Chi-restraints excluded: chain C residue  287 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   chunk 84 optimal weight:    4.9990
   chunk 54 optimal weight:    0.1980
   chunk 32 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 79 optimal weight:    0.0670
   chunk 17 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.4318

-------------------------------------------------------------------------------
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 = 0.091320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.074050 restraints weight = 11887.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 2.22
r_work: 0.2716 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2580 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8965
moved from start:          0.1285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7953  Z= 0.173
  Angle     :  0.484   5.361  10845  Z= 0.257
  Chirality :  0.045   0.124   1197
  Planarity :  0.004   0.030   1422
  Dihedral  :  4.612  26.348   1075
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 13.48 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.23), residues: 996
  helix: -1.10 (0.59), residues: 69
  sheet:  0.60 (0.30), residues: 261
  loop : -1.28 (0.20), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 265 
 HIS   0.004   0.001   HIS C 306 
 PHE   0.010   0.001   PHE C 320 
 TYR   0.008   0.001   TYR A 263 
 ARG   0.002   0.000   ARG C 159 

*********************** 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
  100 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 66
  time to evaluate  : 0.907 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8664 (mm-40)
REVERT: B  113 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8447 (mt0)
REVERT: C  113 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8474 (mt0)
REVERT: C  165 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7894 (pm20)
  outliers start: 34
  outliers final: 8
  residues processed: 91
  average time/residue: 1.1338
  time to fit residues: 110.1491
Evaluate side-chains
  68 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
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  328 ASP
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   94 LEU
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 45 optimal weight:    0.7980
   chunk 1 optimal weight:    0.4980
   chunk 67 optimal weight:    0.0970
   chunk 73 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 74 optimal weight:    0.0030
   chunk 49 optimal weight:    0.5980
   chunk 10 optimal weight:    0.4980
   chunk 71 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.3388

-------------------------------------------------------------------------------
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 = 0.3131 r_free = 0.3131 target = 0.092434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.075201 restraints weight = 11751.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 2.21
r_work: 0.2732 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2596 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8948
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7953  Z= 0.157
  Angle     :  0.481   5.393  10845  Z= 0.256
  Chirality :  0.045   0.127   1197
  Planarity :  0.004   0.029   1422
  Dihedral  :  4.395  24.916   1075
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.07 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.24), residues: 996
  helix: -0.94 (0.58), residues: 72
  sheet:  0.89 (0.30), residues: 261
  loop : -0.99 (0.21), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 265 
 HIS   0.004   0.001   HIS C 306 
 PHE   0.010   0.001   PHE B 320 
 TYR   0.008   0.001   TYR B 263 
 ARG   0.003   0.000   ARG A 253 

*********************** 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
  82 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 54
  time to evaluate  : 0.881 
Fit side-chains
REVERT: B  113 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8469 (mt0)
REVERT: C  113 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8504 (mt0)
REVERT: C  165 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7876 (pm20)
  outliers start: 28
  outliers final: 10
  residues processed: 73
  average time/residue: 1.3572
  time to fit residues: 106.2201
Evaluate side-chains
  65 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
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  131 VAL
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  170 LEU
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   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 30 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 78 optimal weight:    0.4980
   chunk 38 optimal weight:    0.0270
   chunk 15 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.6840

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.090769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.073412 restraints weight = 11785.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.2824 rms_B_bonded: 2.22
r_work: 0.2702 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2566 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8974
moved from start:          0.1461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7953  Z= 0.236
  Angle     :  0.507   5.529  10845  Z= 0.271
  Chirality :  0.046   0.140   1197
  Planarity :  0.004   0.031   1422
  Dihedral  :  4.584  26.795   1075
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 15.07 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.24), residues: 996
  helix: -0.67 (0.61), residues: 69
  sheet:  1.07 (0.30), residues: 261
  loop : -0.94 (0.22), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 265 
 HIS   0.006   0.001   HIS C 306 
 PHE   0.011   0.001   PHE C 320 
 TYR   0.012   0.001   TYR B 134 
 ARG   0.003   0.000   ARG B 253 

*********************** 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: 29
    poor density    : 55
  time to evaluate  : 0.866 
Fit side-chains
REVERT: B  113 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8497 (mt0)
REVERT: B  165 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7749 (pm20)
REVERT: B  170 LEU cc_start: 0.9056 (mp) cc_final: 0.8793 (mt)
REVERT: C  113 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8531 (mt0)
REVERT: C  165 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7954 (pm20)
  outliers start: 29
  outliers final: 12
  residues processed: 74
  average time/residue: 1.2101
  time to fit residues: 95.3344
Evaluate side-chains
  70 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
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  131 VAL
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  328 ASP
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  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 92 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 26 optimal weight:    0.4980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3092 r_free = 0.3092 target = 0.089906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.072642 restraints weight = 11700.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.2808 rms_B_bonded: 2.19
r_work: 0.2689 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2553 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8984
moved from start:          0.1480

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= 0.309
  Angle     :  0.538   5.639  10845  Z= 0.289
  Chirality :  0.047   0.150   1197
  Planarity :  0.004   0.033   1422
  Dihedral  :  4.774  27.835   1075
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.44 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.25), residues: 996
  helix: -0.68 (0.62), residues: 69
  sheet:  1.01 (0.30), residues: 267
  loop : -0.95 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 265 
 HIS   0.006   0.001   HIS C 306 
 PHE   0.012   0.002   PHE C 320 
 TYR   0.014   0.001   TYR B 134 
 ARG   0.002   0.000   ARG B 253 

*********************** 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
  83 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 55
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8203 (mt0)
REVERT: B  113 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8497 (mt0)
REVERT: B  165 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7827 (pm20)
REVERT: B  170 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8862 (mt)
REVERT: C  113 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8564 (mt0)
REVERT: C  165 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8049 (pm20)
REVERT: C  340 MET cc_start: 0.5856 (OUTLIER) cc_final: 0.5186 (tmt)
  outliers start: 28
  outliers final: 13
  residues processed: 75
  average time/residue: 1.3049
  time to fit residues: 104.1779
Evaluate side-chains
  73 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
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 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  170 LEU
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   94 LEU
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  165 GLU
Chi-restraints excluded: chain C residue  340 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 96 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3102 r_free = 0.3102 target = 0.090480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.073188 restraints weight = 11506.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 2.20
r_work: 0.2698 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2561 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8978
moved from start:          0.1507

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= 0.314
  Angle     :  0.544   5.639  10845  Z= 0.292
  Chirality :  0.047   0.149   1197
  Planarity :  0.004   0.034   1422
  Dihedral  :  4.825  27.879   1075
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 16.30 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.24), residues: 996
  helix: -0.73 (0.61), residues: 69
  sheet:  1.00 (0.29), residues: 267
  loop : -0.96 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 265 
 HIS   0.006   0.001   HIS C 306 
 PHE   0.012   0.002   PHE C 320 
 TYR   0.013   0.001   TYR B 134 
 ARG   0.002   0.000   ARG B 253 

*********************** 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
  85 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 55
  time to evaluate  : 0.952 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8236 (mt0)
REVERT: B  113 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8508 (mt0)
REVERT: B  165 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7931 (pm20)
REVERT: B  170 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8841 (mt)
REVERT: C  113 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8598 (mt0)
REVERT: C  165 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8063 (pm20)
  outliers start: 30
  outliers final: 15
  residues processed: 78
  average time/residue: 1.3072
  time to fit residues: 108.7946
Evaluate side-chains
  74 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 53
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
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 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  170 LEU
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   94 LEU
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  165 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 43 optimal weight:    0.4980
   chunk 48 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3114 r_free = 0.3114 target = 0.091089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.073801 restraints weight = 11434.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 2.20
r_work: 0.2714 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2576 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8968
moved from start:          0.1567

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= 0.256
  Angle     :  0.527   5.555  10845  Z= 0.282
  Chirality :  0.046   0.139   1197
  Planarity :  0.004   0.034   1422
  Dihedral  :  4.717  27.165   1075
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 16.91 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.25), residues: 996
  helix: -0.65 (0.61), residues: 69
  sheet:  1.05 (0.29), residues: 267
  loop : -0.89 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 265 
 HIS   0.005   0.001   HIS C 306 
 PHE   0.011   0.002   PHE C 320 
 TYR   0.012   0.001   TYR B 134 
 ARG   0.002   0.000   ARG B 253 

*********************** 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: 28
    poor density    : 55
  time to evaluate  : 0.842 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8217 (mt0)
REVERT: B  113 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8514 (mt0)
REVERT: C  113 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8578 (mt0)
REVERT: C  165 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8021 (pm20)
  outliers start: 28
  outliers final: 17
  residues processed: 76
  average time/residue: 1.2700
  time to fit residues: 102.5532
Evaluate side-chains
  73 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 52
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
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  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  170 LEU
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   94 LEU
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  165 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 81 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0870
   chunk 15 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.3129 r_free = 0.3129 target = 0.091996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.074668 restraints weight = 11566.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 2.22
r_work: 0.2728 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2589 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8958
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7953  Z= 0.215
  Angle     :  0.511   5.501  10845  Z= 0.273
  Chirality :  0.046   0.132   1197
  Planarity :  0.004   0.035   1422
  Dihedral  :  4.599  26.433   1075
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.77 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.25), residues: 996
  helix: -0.55 (0.61), residues: 69
  sheet:  1.27 (0.30), residues: 261
  loop : -0.83 (0.22), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 265 
 HIS   0.005   0.001   HIS B 306 
 PHE   0.011   0.001   PHE B 320 
 TYR   0.010   0.001   TYR B 134 
 ARG   0.002   0.000   ARG B 253 

*********************** 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
  76 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 54
  time to evaluate  : 0.874 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8197 (mt0)
REVERT: B  113 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8528 (mt0)
REVERT: C  113 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8587 (mt0)
REVERT: C  165 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.7961 (pm20)
  outliers start: 22
  outliers final: 14
  residues processed: 68
  average time/residue: 1.2528
  time to fit residues: 90.7824
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  : 0.867 
-------------------------------------------------------------------------------
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  175 ILE
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  170 LEU
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   94 LEU
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  165 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 85 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0980
   chunk 43 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3134 r_free = 0.3134 target = 0.092353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.074979 restraints weight = 11554.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 2.21
r_work: 0.2734 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2599 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8967
moved from start:          0.1682

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= 0.207
  Angle     :  0.509   5.474  10845  Z= 0.271
  Chirality :  0.045   0.131   1197
  Planarity :  0.004   0.035   1422
  Dihedral  :  4.547  26.216   1075
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.38 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.25), residues: 996
  helix: -0.46 (0.61), residues: 69
  sheet:  1.30 (0.29), residues: 261
  loop : -0.77 (0.22), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 265 
 HIS   0.004   0.001   HIS C 306 
 PHE   0.011   0.001   PHE B 320 
 TYR   0.010   0.001   TYR B 134 
 ARG   0.002   0.000   ARG B 253 

********************** 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
  74 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 55
  time to evaluate  : 0.861 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8187 (mt0)
REVERT: B  113 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8512 (mt0)
REVERT: C  113 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8565 (mt0)
REVERT: C  165 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.7915 (pm20)
  outliers start: 19
  outliers final: 13
  residues processed: 68
  average time/residue: 1.2887
  time to fit residues: 93.2579
Evaluate side-chains
  69 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
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  175 ILE
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  170 LEU
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   94 LEU
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  165 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 66 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   chunk 50 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.091683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.074380 restraints weight = 11425.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 2.21
r_work: 0.2723 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2586 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8960
moved from start:          0.1668

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= 0.246
  Angle     :  0.524   5.603  10845  Z= 0.280
  Chirality :  0.046   0.139   1197
  Planarity :  0.004   0.035   1422
  Dihedral  :  4.656  27.086   1075
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.01 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.25), residues: 996
  helix: -0.49 (0.61), residues: 69
  sheet:  1.30 (0.30), residues: 261
  loop : -0.77 (0.22), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 265 
 HIS   0.005   0.001   HIS C 306 
 PHE   0.011   0.002   PHE C 320 
 TYR   0.012   0.001   TYR B 134 
 ARG   0.002   0.000   ARG B 253 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4973.42 seconds
wall clock time: 89 minutes 19.49 seconds (5359.49 seconds total)