Starting phenix.real_space_refine
on Sat Aug 23 06:37:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p12_17343/08_2025/8p12_17343.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p12_17343/08_2025/8p12_17343.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p12_17343/08_2025/8p12_17343.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p12_17343/08_2025/8p12_17343.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p12_17343/08_2025/8p12_17343.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p12_17343/08_2025/8p12_17343.map"
  }
  resolution = 3.21
  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=  -0.001 sd=   0.019
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: 4
    Type Number    sf(0)   Gaussians
     S      77      5.16       5
     C    6549      2.51       5
     N    1700      2.21       5
     O    1940      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10266
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2530
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2530
          Classifications: {'peptide': 317}
          Link IDs: {'PTRANS': 18, 'TRANS': 298}
    Chain: "A"
      Number of atoms: 1699
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 210, 1693
          Classifications: {'peptide': 210}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 207}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
      Conformer: "B"
        Number of residues, atoms: 210, 1693
          Classifications: {'peptide': 210}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 207}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
          bond proxies already assigned to first conformer: 1714
    Chain: "B"
      Number of atoms: 2416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2416
          Classifications: {'peptide': 316}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 310}
    Chain: "G"
      Number of atoms: 293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 293
          Classifications: {'peptide': 36}
          Link IDs: {'PTRANS': 3, 'TRANS': 32}
    Chain: "L"
      Number of atoms: 1699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1699
          Classifications: {'peptide': 219}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207}
    Chain: "H"
      Number of atoms: 1629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1629
          Classifications: {'peptide': 218}
          Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 202}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ACYS A 305 " occ=0.57
      ... (10 atoms not shown)
      pdb=" SG BCYS A 305 " occ=0.43
  Time building chain proxies: 2.57, per 1000 atoms: 0.25
  Number of scatterers: 10266
  At special positions: 0
  Unit cell: (100.1, 115.7, 141.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      77     16.00
     O    1940      8.00
     N    1700      7.00
     C    6549      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS R   2 " - pdb=" SG  CYS R 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 110 " - pdb=" SG  CYS R 187 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  42 " - pdb=" SG  CYS L 112 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 158 " - pdb=" SG  CYS L 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 114 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 165 " - pdb=" SG  CYS H 220 " distance=2.03

  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: 0.96
  Conformation dependent library (CDL) restraints added in 283.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2446

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 19 sheets defined
      32.0% alpha, 26.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'R' and resid 33 through 65
      Proline residue:  R  53  - end of helix
      removed outlier: 3.692A  pdb=" N   LEU R  59 " --> pdb=" O   ASN R  55 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 69
    Processing helix  chain 'R' and resid 70 through 72
      No H-bonds generated for 'chain 'R' and resid 70 through 72'
    Processing helix  chain 'R' and resid 73 through 90
    Processing helix  chain 'R' and resid 90 through 99
    Processing helix  chain 'R' and resid 105 through 141
    Processing helix  chain 'R' and resid 149 through 169
    Processing helix  chain 'R' and resid 199 through 211
    Processing helix  chain 'R' and resid 212 through 237
    Processing helix  chain 'R' and resid 240 through 278
      Proline residue:  R 267  - end of helix
    Processing helix  chain 'R' and resid 284 through 290
    Processing helix  chain 'R' and resid 290 through 297
    Processing helix  chain 'R' and resid 297 through 307
      Proline residue:  R 303  - end of helix
    Processing helix  chain 'R' and resid 310 through 317
    Processing helix  chain 'A' and resid 5 through 33
    Processing helix  chain 'A' and resid 45 through 58
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.158A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 243 through 255
    Processing helix  chain 'A' and resid 256 through 261
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.597A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 296 through 309
    Processing helix  chain 'A' and resid 327 through 351
      removed outlier: 3.508A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 32 through 48
      removed outlier: 3.645A  pdb=" N   CYS G  36 " --> pdb=" O   LEU G  32 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ARG G  47 " --> pdb=" O   TYR G  43 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 51 through 56
      removed outlier: 3.916A  pdb=" N   LYS G  55 " --> pdb=" O   ASP G  51 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 103 through 107
      removed outlier: 3.550A  pdb=" N   LEU L 107 " --> pdb=" O   ALA L 104 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 145 through 152
    Processing helix  chain 'L' and resid 206 through 212
    Processing helix  chain 'H' and resid 105 through 109
    Processing sheet with id=AA1, first strand: chain 'R' and resid 4 through 5
    Processing sheet with id=AA2, first strand: chain 'R' and resid 178 through 181
      removed outlier: 4.389A  pdb=" N   SER R 186 " --> pdb=" O   GLU R 181 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 191
      removed outlier: 8.845A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 9.042A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.388A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 9.034A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.620A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.783A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.650A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.983A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.769A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 234
      removed outlier: 3.788A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   CYS B 233 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.146A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 23 through 26
      removed outlier: 3.636A  pdb=" N   THR L  24 " --> pdb=" O   ARG L  43 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE L  40 " --> pdb=" O   LEU L  97 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   CYS L  42 " --> pdb=" O   PHE L  95 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   PHE L  95 " --> pdb=" O   CYS L  42 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 29 through 32
      removed outlier: 3.946A  pdb=" N   GLU L 129 " --> pdb=" O   LEU L  30 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   GLY L 108 " --> pdb=" O   LEU L 128 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   LEU L  57 " --> pdb=" O   TYR L  73 " (cutoff:3.500A)
      removed outlier: 5.281A  pdb=" N   TYR L  73 " --> pdb=" O   LEU L  57 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   TRP L  59 " --> pdb=" O   LEU L  71 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 29 through 32
      removed outlier: 3.946A  pdb=" N   GLU L 129 " --> pdb=" O   LEU L  30 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   GLY L 108 " --> pdb=" O   LEU L 128 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   THR L 121 " --> pdb=" O   GLN L 114 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 138 through 142
      removed outlier: 3.740A  pdb=" N   VAL L 157 " --> pdb=" O   PHE L 142 " (cutoff:3.500A)
      removed outlier: 5.506A  pdb=" N   SER L 155 " --> pdb=" O   LEU L 205 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   LEU L 205 " --> pdb=" O   SER L 155 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   VAL L 157 " --> pdb=" O   LEU L 203 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   LEU L 203 " --> pdb=" O   VAL L 157 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   PHE L 159 " --> pdb=" O   SER L 201 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   SER L 201 " --> pdb=" O   PHE L 159 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   ASN L 161 " --> pdb=" O   MET L 199 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   MET L 199 " --> pdb=" O   ASN L 161 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 177 through 179
      removed outlier: 3.804A  pdb=" N   TYR L 216 " --> pdb=" O   PHE L 233 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   PHE L 233 " --> pdb=" O   TYR L 216 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 22 through 26
      removed outlier: 3.887A  pdb=" N   VAL H  97 " --> pdb=" O   CYS H  41 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 30 through 31
      removed outlier: 3.574A  pdb=" N   THR H 132 " --> pdb=" O   TYR H 112 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   TYR H 112 " --> pdb=" O   THR H 132 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA H 110 " --> pdb=" O   VAL H 134 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY H  68 " --> pdb=" O   TRP H  55 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ARG H  57 " --> pdb=" O   TRP H  66 " (cutoff:3.500A)
      removed outlier: 5.688A  pdb=" N   TRP H  66 " --> pdb=" O   ARG H  57 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 146 through 149
      removed outlier: 3.578A  pdb=" N   TYR H 147 " --> pdb=" O   LEU H 166 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU H 166 " --> pdb=" O   TYR H 147 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   VAL H 208 " --> pdb=" O   VAL H 161 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU H 163 " --> pdb=" O   VAL H 206 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   GLY H 169 " --> pdb=" O   TYR H 200 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   TYR H 200 " --> pdb=" O   GLY H 169 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   LEU H 199 " --> pdb=" O   LEU H 195 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   LEU H 195 " --> pdb=" O   LEU H 199 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   THR H 201 " --> pdb=" O   ALA H 193 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   ALA H 193 " --> pdb=" O   THR H 201 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   SER H 203 " --> pdb=" O   PHE H 191 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 176 through 179
      removed outlier: 3.516A  pdb=" N   ALA H 223 " --> pdb=" O   THR H 176 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL H 231 " --> pdb=" O   VAL H 222 " (cutoff:3.500A)

    479 hydrogen bonds defined for protein.
    1336 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: 1.42

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        0.88 -     1.07: 1
        1.07 -     1.26: 1671
        1.26 -     1.45: 2988
        1.45 -     1.64: 5742
        1.64 -     1.83: 111
  Bond restraints: 10513
  Sorted by residual:
  bond pdb=" CB  PRO R 291 "
       pdb=" CG  PRO R 291 "
    ideal  model  delta    sigma   weight residual
    1.492  0.879  0.613 5.00e-02 4.00e+02 1.50e+02
  bond pdb=" CG  PRO R 291 "
       pdb=" CD  PRO R 291 "
    ideal  model  delta    sigma   weight residual
    1.503  1.214  0.289 3.40e-02 8.65e+02 7.22e+01
  bond pdb=" CG  PRO G  58 "
       pdb=" CD  PRO G  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.360  0.143 3.40e-02 8.65e+02 1.76e+01
  bond pdb=" N   PRO R 291 "
       pdb=" CA  PRO R 291 "
    ideal  model  delta    sigma   weight residual
    1.471  1.508 -0.037 1.29e-02 6.01e+03 8.06e+00
  bond pdb=" C   ILE R 290 "
       pdb=" N   PRO R 291 "
    ideal  model  delta    sigma   weight residual
    1.336  1.357 -0.021 1.20e-02 6.94e+03 3.08e+00
  ... (remaining 10508 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    10.44: 14259
       10.44 -    20.89: 10
       20.89 -    31.33: 1
       31.33 -    41.77: 1
       41.77 -    52.21: 1
  Bond angle restraints: 14272
  Sorted by residual:
  angle pdb=" N   PRO R 291 "
        pdb=" CD  PRO R 291 "
        pdb=" CG  PRO R 291 "
      ideal   model   delta    sigma   weight residual
     103.20   77.39   25.81 1.50e+00 4.44e-01 2.96e+02
  angle pdb=" CA  PRO R 291 "
        pdb=" CB  PRO R 291 "
        pdb=" CG  PRO R 291 "
      ideal   model   delta    sigma   weight residual
     104.50   72.93   31.57 1.90e+00 2.77e-01 2.76e+02
  angle pdb=" CB  PRO R 291 "
        pdb=" CG  PRO R 291 "
        pdb=" CD  PRO R 291 "
      ideal   model   delta    sigma   weight residual
     106.10  158.31  -52.21 3.20e+00 9.77e-02 2.66e+02
  angle pdb=" N   PRO G  58 "
        pdb=" CD  PRO G  58 "
        pdb=" CG  PRO G  58 "
      ideal   model   delta    sigma   weight residual
     103.20   90.48   12.72 1.50e+00 4.44e-01 7.20e+01
  angle pdb=" CA  PRO R 291 "
        pdb=" N   PRO R 291 "
        pdb=" CD  PRO R 291 "
      ideal   model   delta    sigma   weight residual
     112.00  101.02   10.98 1.40e+00 5.10e-01 6.15e+01
  ... (remaining 14267 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 5533
       17.27 -    34.55: 490
       34.55 -    51.82: 137
       51.82 -    69.09: 26
       69.09 -    86.37: 17
  Dihedral angle restraints: 6203
    sinusoidal: 2396
      harmonic: 3807
  Sorted by residual:
  dihedral pdb=" CB  CYS H 165 "
           pdb=" SG  CYS H 165 "
           pdb=" SG  CYS H 220 "
           pdb=" CB  CYS H 220 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.19   61.19     1      1.00e+01 1.00e-02 4.97e+01
  dihedral pdb=" N   PRO R 291 "
           pdb=" CG  PRO R 291 "
           pdb=" CD  PRO R 291 "
           pdb=" CB  PRO R 291 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00 -114.27   84.27     1      1.50e+01 4.44e-03 3.84e+01
  dihedral pdb=" CB  CYS R 110 "
           pdb=" SG  CYS R 110 "
           pdb=" SG  CYS R 187 "
           pdb=" CB  CYS R 187 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.93   35.93     1      1.00e+01 1.00e-02 1.83e+01
  ... (remaining 6200 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1272
       0.057 -    0.114: 293
       0.114 -    0.171: 22
       0.171 -    0.228: 5
       0.228 -    0.285: 5
  Chirality restraints: 1597
  Sorted by residual:
  chirality pdb=" CB  ILE A 343 "
            pdb=" CA  ILE A 343 "
            pdb=" CG1 ILE A 343 "
            pdb=" CG2 ILE A 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.29 2.00e-01 2.50e+01 2.04e+00
  chirality pdb=" CA  ILE R 290 "
            pdb=" N   ILE R 290 "
            pdb=" C   ILE R 290 "
            pdb=" CB  ILE R 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.18    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CB  VAL R 162 "
            pdb=" CA  VAL R 162 "
            pdb=" CG1 VAL R 162 "
            pdb=" CG2 VAL R 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.50e+00
  ... (remaining 1594 not shown)

  Planarity restraints: 1813
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN R 312 "   -0.030 2.00e-02 2.50e+03   6.02e-02 3.63e+01
        pdb=" C   GLN R 312 "    0.104 2.00e-02 2.50e+03
        pdb=" O   GLN R 312 "   -0.039 2.00e-02 2.50e+03
        pdb=" N   PHE R 313 "   -0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS R 311 "   -0.025 2.00e-02 2.50e+03   4.86e-02 2.36e+01
        pdb=" C   LYS R 311 "    0.084 2.00e-02 2.50e+03
        pdb=" O   LYS R 311 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   GLN R 312 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN R 315 "   -0.017 2.00e-02 2.50e+03   3.28e-02 1.07e+01
        pdb=" C   ASN R 315 "    0.057 2.00e-02 2.50e+03
        pdb=" O   ASN R 315 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   CYS R 316 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1810 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 272
        2.67 -     3.23: 10317
        3.23 -     3.79: 16811
        3.79 -     4.34: 22364
        4.34 -     4.90: 36180
  Nonbonded interactions: 85944
  Sorted by model distance:
  nonbonded pdb=" OG1 THR R 242 "
            pdb=" OE1 GLU A 318 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" O   TRP A 258 "
            pdb=" OG1 THR A 262 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" O   TYR L 210 "
            pdb=" OH  TYR L 216 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   MET B 325 "
            pdb=" ND2 ASN B 340 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" O   TRP R 175 "
            pdb=" OG  SER R 176 "
     model   vdw
     2.224 3.040
  ... (remaining 85939 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.43 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.990
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.220
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6742
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      :  0.008   0.613  10519  Z= 0.237
  Angle     :  1.109  52.214  14284  Z= 0.593
  Chirality :  0.048   0.285   1597
  Planarity :  0.006   0.061   1813
  Dihedral  : 15.144  86.366   3739
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 17.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  : 18.69 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.37 (0.23), residues: 1301
  helix:  0.09 (0.26), residues: 360
  sheet:  0.60 (0.28), residues: 341
  loop : -0.90 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 134 
 TYR   0.019   0.002   TYR R 136 
 PHE   0.037   0.002   PHE R 294 
 TRP   0.018   0.002   TRP R 175 
 HIS   0.008   0.001   HIS R 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00769 (10513)
  covalent geometry    : angle       1.10876 (14272)
  SS BOND              : bond        0.00353 (    6)
  SS BOND              : angle       1.03555 (   12)
  hydrogen bonds       : bond        0.16626 (  474)
  hydrogen bonds       : angle       8.34696 ( 1336)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R    1 MET cc_start: 0.6853 (ppp) cc_final: 0.6474 (ppp)
REVERT: R   86 MET cc_start: 0.3565 (tpt) cc_final: 0.3120 (tpt)
REVERT: R  155 MET cc_start: 0.7990 (ttt) cc_final: 0.7366 (ptm)
REVERT: R  308 MET cc_start: 0.8548 (mmm) cc_final: 0.7471 (tpt)
REVERT: R  317 MET cc_start: 0.5524 (ppp) cc_final: 0.4383 (ppp)
REVERT: A   10 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7191 (mmmt)
REVERT: A  354 PHE cc_start: 0.1987 (m-80) cc_final: 0.0459 (p90)
REVERT: B  117 LEU cc_start: 0.7212 (mt) cc_final: 0.6528 (pp)
  outliers start: 1
  outliers final: 1
  residues processed: 112
  average time/residue: 0.0882
  time to fit residues: 14.5704
Evaluate side-chains
  93 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  128 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.6980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.0870
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   overall best weight:    1.2762

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

Flipped N/Q/H residues before XYZ refinement:
** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  57 HIS
A 256 ASN
A 306 GLN
B 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.116419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.095011 restraints weight = 74798.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.4042 rms_B_bonded: 6.31
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4043 r_free = 0.4043    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4043 r_free = 0.4043    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6842
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10519  Z= 0.193
  Angle     :  0.711  13.865  14284  Z= 0.370
  Chirality :  0.045   0.216   1597
  Planarity :  0.005   0.057   1813
  Dihedral  :  5.096  25.653   1412
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.75 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.01 (0.23), residues: 1301
  helix:  0.81 (0.26), residues: 368
  sheet:  0.48 (0.27), residues: 348
  loop : -0.78 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 150 
 TYR   0.035   0.002   TYR A 302 
 PHE   0.021   0.002   PHE R  91 
 TRP   0.020   0.002   TRP B 169 
 HIS   0.006   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (10513)
  covalent geometry    : angle       0.71119 (14272)
  SS BOND              : bond        0.00147 (    6)
  SS BOND              : angle       0.99974 (   12)
  hydrogen bonds       : bond        0.04388 (  474)
  hydrogen bonds       : angle       6.68510 ( 1336)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   91 PHE cc_start: 0.8320 (m-10) cc_final: 0.8099 (m-10)
REVERT: R  155 MET cc_start: 0.8052 (ttt) cc_final: 0.7369 (ptt)
REVERT: R  181 GLU cc_start: 0.7707 (pp20) cc_final: 0.7352 (pm20)
REVERT: R  291 PRO cc_start: 0.7084 (Cg_exo) cc_final: 0.6849 (Cg_endo)
REVERT: R  308 MET cc_start: 0.8565 (mmm) cc_final: 0.7438 (tpt)
REVERT: B  117 LEU cc_start: 0.7383 (mt) cc_final: 0.6902 (pp)
  outliers start: 25
  outliers final: 20
  residues processed: 116
  average time/residue: 0.0791
  time to fit residues: 13.6434
Evaluate side-chains
  112 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   81 VAL
Chi-restraints excluded: chain R residue   96 TYR
Chi-restraints excluded: chain R residue  250 VAL
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain G residue   32 LEU
Chi-restraints excluded: chain L residue   84 ASP
Chi-restraints excluded: chain L residue  129 GLU
Chi-restraints excluded: chain L residue  230 VAL
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  140 LYS
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  204 SER
Chi-restraints excluded: chain H residue  228 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0980
   chunk 89 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 81 optimal weight:    0.9980
   chunk 84 optimal weight:    0.2980
   chunk 25 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 97 optimal weight:    0.0980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
R 195 HIS
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.117710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.095725 restraints weight = 96336.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.4057 rms_B_bonded: 7.33
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4058
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4058 r_free = 0.4058    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4058 r_free = 0.4058    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4058
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6798
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10519  Z= 0.128
  Angle     :  0.642  12.902  14284  Z= 0.327
  Chirality :  0.043   0.186   1597
  Planarity :  0.005   0.050   1813
  Dihedral  :  4.699  23.098   1410
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 17.99 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.12 (0.23), residues: 1301
  helix:  0.96 (0.26), residues: 368
  sheet:  0.61 (0.27), residues: 363
  loop : -0.81 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  68 
 TYR   0.035   0.001   TYR A 302 
 PHE   0.017   0.001   PHE R 148 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.003   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (10513)
  covalent geometry    : angle       0.64182 (14272)
  SS BOND              : bond        0.00107 (    6)
  SS BOND              : angle       0.81212 (   12)
  hydrogen bonds       : bond        0.03789 (  474)
  hydrogen bonds       : angle       6.22213 ( 1336)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R    1 MET cc_start: 0.7018 (ppp) cc_final: 0.6658 (ppp)
REVERT: R   40 LEU cc_start: 0.9168 (tt) cc_final: 0.8928 (pp)
REVERT: R   86 MET cc_start: 0.4196 (tpt) cc_final: 0.3700 (tpp)
REVERT: R  155 MET cc_start: 0.8080 (ttt) cc_final: 0.7344 (ptp)
REVERT: R  308 MET cc_start: 0.8617 (mmm) cc_final: 0.7388 (tpt)
REVERT: B  117 LEU cc_start: 0.7306 (mt) cc_final: 0.6773 (pp)
REVERT: L  191 ASP cc_start: 0.7593 (t0) cc_final: 0.7346 (t0)
  outliers start: 23
  outliers final: 16
  residues processed: 124
  average time/residue: 0.0728
  time to fit residues: 13.4669
Evaluate side-chains
  109 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   81 VAL
Chi-restraints excluded: chain R residue   96 TYR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain G residue   32 LEU
Chi-restraints excluded: chain L residue  129 GLU
Chi-restraints excluded: chain L residue  230 VAL
Chi-restraints excluded: chain H residue  165 CYS
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  204 SER
Chi-restraints excluded: chain H residue  218 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0470
   chunk 113 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 108 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 83 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.6080

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.117680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.097164 restraints weight = 59772.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.4093 rms_B_bonded: 5.63
r_work (final): 0.4093
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4093
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4093 r_free = 0.4093    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4093 r_free = 0.4093    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4093
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6771
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10519  Z= 0.131
  Angle     :  0.630  12.846  14284  Z= 0.320
  Chirality :  0.043   0.200   1597
  Planarity :  0.004   0.051   1813
  Dihedral  :  4.604  25.330   1410
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.72 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.14 (0.23), residues: 1301
  helix:  1.02 (0.27), residues: 368
  sheet:  0.55 (0.27), residues: 369
  loop : -0.78 (0.27), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 283 
 TYR   0.033   0.001   TYR A 302 
 PHE   0.015   0.001   PHE R  91 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (10513)
  covalent geometry    : angle       0.63036 (14272)
  SS BOND              : bond        0.00091 (    6)
  SS BOND              : angle       0.77281 (   12)
  hydrogen bonds       : bond        0.03676 (  474)
  hydrogen bonds       : angle       6.00227 ( 1336)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R    1 MET cc_start: 0.7052 (ppp) cc_final: 0.6757 (ppp)
REVERT: R   40 LEU cc_start: 0.9178 (tt) cc_final: 0.8957 (pp)
REVERT: R  155 MET cc_start: 0.8071 (ttt) cc_final: 0.7358 (ptm)
REVERT: B  117 LEU cc_start: 0.7253 (mt) cc_final: 0.6757 (pp)
REVERT: B  211 TRP cc_start: 0.6175 (OUTLIER) cc_final: 0.5882 (m100)
REVERT: H  179 TRP cc_start: 0.6442 (m100) cc_final: 0.6229 (m100)
  outliers start: 26
  outliers final: 20
  residues processed: 115
  average time/residue: 0.0782
  time to fit residues: 13.5136
Evaluate side-chains
  114 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   81 VAL
Chi-restraints excluded: chain R residue   96 TYR
Chi-restraints excluded: chain R residue  276 PHE
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain G residue   62 ASN
Chi-restraints excluded: chain L residue  129 GLU
Chi-restraints excluded: chain L residue  230 VAL
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  165 CYS
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  204 SER
Chi-restraints excluded: chain H residue  218 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 85 optimal weight:    8.9990
   chunk 59 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 123 optimal weight:    8.9990
   chunk 33 optimal weight:    3.9990
   chunk 121 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
L 180 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.112472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.091178 restraints weight = 58505.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3972 rms_B_bonded: 5.42
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3972
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3972 r_free = 0.3972    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3972 r_free = 0.3972    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3972
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.100  10519  Z= 0.383
  Angle     :  0.864  10.345  14284  Z= 0.455
  Chirality :  0.050   0.209   1597
  Planarity :  0.006   0.061   1813
  Dihedral  :  5.684  30.336   1410
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 23.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 17.72 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    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: -0.63 (0.23), residues: 1301
  helix:  0.27 (0.26), residues: 369
  sheet:  0.17 (0.28), residues: 326
  loop : -1.13 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  15 
 TYR   0.038   0.003   TYR H 119 
 PHE   0.033   0.003   PHE R  91 
 TRP   0.022   0.004   TRP B 211 
 HIS   0.021   0.003   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00845 (10513)
  covalent geometry    : angle       0.86284 (14272)
  SS BOND              : bond        0.00328 (    6)
  SS BOND              : angle       1.59156 (   12)
  hydrogen bonds       : bond        0.05213 (  474)
  hydrogen bonds       : angle       6.76963 ( 1336)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 91
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R    1 MET cc_start: 0.7377 (ppp) cc_final: 0.6990 (ppp)
REVERT: R   40 LEU cc_start: 0.9145 (tt) cc_final: 0.8868 (pp)
REVERT: R  155 MET cc_start: 0.8082 (ttt) cc_final: 0.7178 (ptm)
REVERT: R  214 ILE cc_start: 0.8266 (mm) cc_final: 0.8007 (mm)
REVERT: R  268 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.6671 (m-80)
REVERT: R  308 MET cc_start: 0.8376 (mmm) cc_final: 0.6829 (tpt)
REVERT: R  317 MET cc_start: 0.6432 (ppp) cc_final: 0.5850 (ppp)
REVERT: B   54 HIS cc_start: 0.4066 (OUTLIER) cc_final: 0.2737 (m-70)
REVERT: L  191 ASP cc_start: 0.8023 (t0) cc_final: 0.7734 (t0)
REVERT: H  160 MET cc_start: 0.8763 (tmm) cc_final: 0.8420 (tmm)
  outliers start: 44
  outliers final: 26
  residues processed: 123
  average time/residue: 0.0863
  time to fit residues: 15.7162
Evaluate side-chains
  116 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   81 VAL
Chi-restraints excluded: chain R residue   96 TYR
Chi-restraints excluded: chain R residue  245 LYS
Chi-restraints excluded: chain R residue  250 VAL
Chi-restraints excluded: chain R residue  268 TYR
Chi-restraints excluded: chain R residue  276 PHE
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain G residue   31 MET
Chi-restraints excluded: chain G residue   62 ASN
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   84 ASP
Chi-restraints excluded: chain L residue  129 GLU
Chi-restraints excluded: chain H residue   54 HIS
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  119 TYR
Chi-restraints excluded: chain H residue  140 LYS
Chi-restraints excluded: chain H residue  165 CYS
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  204 SER
Chi-restraints excluded: chain H residue  218 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 113 optimal weight:    0.5980
   chunk 114 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0870
   chunk 98 optimal weight:    0.9980
   chunk 111 optimal weight:    0.7980
   chunk 72 optimal weight:    0.5980
   chunk 126 optimal weight:    2.9990
   chunk 122 optimal weight:    0.0980
   overall best weight:    0.3958

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.116590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.096420 restraints weight = 57285.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.4083 rms_B_bonded: 5.38
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4082
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4082 r_free = 0.4082    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4082 r_free = 0.4082    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4082
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6801
moved from start:          0.2615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10519  Z= 0.132
  Angle     :  0.660  15.069  14284  Z= 0.333
  Chirality :  0.044   0.177   1597
  Planarity :  0.005   0.050   1813
  Dihedral  :  4.923  25.778   1410
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 19.49 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.27 (0.23), residues: 1301
  helix:  0.64 (0.26), residues: 366
  sheet:  0.20 (0.27), residues: 352
  loop : -0.89 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R  21 
 TYR   0.029   0.001   TYR A 302 
 PHE   0.013   0.001   PHE B 292 
 TRP   0.026   0.002   TRP B 211 
 HIS   0.003   0.001   HIS R 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (10513)
  covalent geometry    : angle       0.65976 (14272)
  SS BOND              : bond        0.00167 (    6)
  SS BOND              : angle       0.95628 (   12)
  hydrogen bonds       : bond        0.03677 (  474)
  hydrogen bonds       : angle       6.23093 ( 1336)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R    1 MET cc_start: 0.7372 (ppp) cc_final: 0.7107 (ppp)
REVERT: R  155 MET cc_start: 0.7843 (ttt) cc_final: 0.6957 (ptp)
REVERT: R  191 TYR cc_start: 0.7491 (p90) cc_final: 0.7266 (p90)
REVERT: R  214 ILE cc_start: 0.8161 (mm) cc_final: 0.7907 (mm)
REVERT: R  308 MET cc_start: 0.8431 (mmm) cc_final: 0.6965 (tpt)
REVERT: R  317 MET cc_start: 0.6546 (ppp) cc_final: 0.5916 (ppp)
REVERT: A  354 PHE cc_start: 0.1844 (m-80) cc_final: 0.0022 (p90)
REVERT: G   31 MET cc_start: 0.6550 (tmm) cc_final: 0.5596 (ttp)
REVERT: H  160 MET cc_start: 0.8443 (tmm) cc_final: 0.7947 (tmm)
  outliers start: 22
  outliers final: 15
  residues processed: 114
  average time/residue: 0.0727
  time to fit residues: 12.8951
Evaluate side-chains
  107 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   96 TYR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain L residue  129 GLU
Chi-restraints excluded: chain H residue   43 VAL
Chi-restraints excluded: chain H residue   92 ASN
Chi-restraints excluded: chain H residue  119 TYR
Chi-restraints excluded: chain H residue  142 THR
Chi-restraints excluded: chain H residue  165 CYS
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  190 THR
Chi-restraints excluded: chain H residue  204 SER
Chi-restraints excluded: chain H residue  228 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 121 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 89 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.113969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.092024 restraints weight = 97660.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 7.18
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3992
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3992 r_free = 0.3992    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3992 r_free = 0.3992    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3992
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6913
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10519  Z= 0.167
  Angle     :  0.661  14.698  14284  Z= 0.337
  Chirality :  0.044   0.177   1597
  Planarity :  0.005   0.052   1813
  Dihedral  :  4.896  27.834   1410
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 15.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 19.84 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.24 (0.23), residues: 1301
  helix:  0.66 (0.26), residues: 370
  sheet:  0.21 (0.28), residues: 328
  loop : -0.84 (0.26), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  15 
 TYR   0.028   0.002   TYR A 302 
 PHE   0.020   0.002   PHE R  91 
 TRP   0.020   0.002   TRP B 211 
 HIS   0.010   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (10513)
  covalent geometry    : angle       0.66056 (14272)
  SS BOND              : bond        0.00140 (    6)
  SS BOND              : angle       0.95709 (   12)
  hydrogen bonds       : bond        0.03755 (  474)
  hydrogen bonds       : angle       6.15737 ( 1336)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: R    1 MET cc_start: 0.7324 (ppp) cc_final: 0.7119 (ppp)
REVERT: R   40 LEU cc_start: 0.9071 (tt) cc_final: 0.8809 (pp)
REVERT: R   86 MET cc_start: 0.4684 (tpt) cc_final: 0.4048 (tpt)
REVERT: R  155 MET cc_start: 0.7874 (ttt) cc_final: 0.6939 (ptp)
REVERT: R  191 TYR cc_start: 0.7712 (p90) cc_final: 0.7495 (p90)
REVERT: R  207 MET cc_start: 0.8523 (mmt) cc_final: 0.8275 (mmm)
REVERT: R  214 ILE cc_start: 0.8224 (mm) cc_final: 0.7965 (mm)
REVERT: R  308 MET cc_start: 0.8530 (mmm) cc_final: 0.7043 (tpt)
REVERT: R  317 MET cc_start: 0.6510 (ppp) cc_final: 0.5949 (ppp)
REVERT: G   31 MET cc_start: 0.6564 (tmm) cc_final: 0.5820 (ttp)
REVERT: L  191 ASP cc_start: 0.7798 (t0) cc_final: 0.7471 (t0)
REVERT: H  160 MET cc_start: 0.8564 (tmm) cc_final: 0.8145 (tmm)
REVERT: H  163 LEU cc_start: 0.8184 (mt) cc_final: 0.7731 (mt)
  outliers start: 22
  outliers final: 19
  residues processed: 114
  average time/residue: 0.0665
  time to fit residues: 11.6968
Evaluate side-chains
  112 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   96 TYR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   84 ASP
Chi-restraints excluded: chain L residue  129 GLU
Chi-restraints excluded: chain H residue   43 VAL
Chi-restraints excluded: chain H residue   92 ASN
Chi-restraints excluded: chain H residue  119 TYR
Chi-restraints excluded: chain H residue  142 THR
Chi-restraints excluded: chain H residue  165 CYS
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  204 SER
Chi-restraints excluded: chain H residue  218 VAL
Chi-restraints excluded: chain H residue  228 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 34 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 67 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 123 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0010
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.115299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.095771 restraints weight = 52375.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.4069 rms_B_bonded: 5.07
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4070 r_free = 0.4070    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4070 r_free = 0.4070    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4070
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6804
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10519  Z= 0.129
  Angle     :  0.663  14.566  14284  Z= 0.331
  Chirality :  0.044   0.291   1597
  Planarity :  0.005   0.050   1813
  Dihedral  :  4.745  25.854   1410
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 20.11 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.12 (0.23), residues: 1301
  helix:  0.80 (0.27), residues: 370
  sheet:  0.20 (0.28), residues: 355
  loop : -0.78 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  15 
 TYR   0.027   0.001   TYR A 302 
 PHE   0.031   0.001   PHE B 292 
 TRP   0.028   0.002   TRP B 211 
 HIS   0.004   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10513)
  covalent geometry    : angle       0.66240 (14272)
  SS BOND              : bond        0.00120 (    6)
  SS BOND              : angle       0.80390 (   12)
  hydrogen bonds       : bond        0.03506 (  474)
  hydrogen bonds       : angle       6.00434 ( 1336)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   40 LEU cc_start: 0.9013 (tt) cc_final: 0.8797 (pp)
REVERT: R   86 MET cc_start: 0.4831 (tpt) cc_final: 0.4298 (tpt)
REVERT: R  155 MET cc_start: 0.7840 (ttt) cc_final: 0.6946 (ptp)
REVERT: R  191 TYR cc_start: 0.7633 (p90) cc_final: 0.7421 (p90)
REVERT: R  207 MET cc_start: 0.8530 (mmt) cc_final: 0.8262 (mmm)
REVERT: R  214 ILE cc_start: 0.8081 (mm) cc_final: 0.7825 (mm)
REVERT: R  253 MET cc_start: 0.6349 (ttt) cc_final: 0.6101 (ttt)
REVERT: R  308 MET cc_start: 0.8409 (mmm) cc_final: 0.6990 (tpt)
REVERT: R  317 MET cc_start: 0.6621 (ppp) cc_final: 0.6182 (ppp)
REVERT: A   10 LYS cc_start: 0.7538 (mmtt) cc_final: 0.7022 (mmmt)
REVERT: G   31 MET cc_start: 0.6104 (tmm) cc_final: 0.5287 (ttp)
REVERT: L  191 ASP cc_start: 0.7623 (t0) cc_final: 0.7392 (t0)
REVERT: H  160 MET cc_start: 0.8458 (tmm) cc_final: 0.8087 (tmm)
REVERT: H  163 LEU cc_start: 0.8221 (mt) cc_final: 0.7708 (mt)
REVERT: H  204 SER cc_start: 0.7727 (OUTLIER) cc_final: 0.7387 (p)
  outliers start: 19
  outliers final: 15
  residues processed: 110
  average time/residue: 0.0899
  time to fit residues: 15.1283
Evaluate side-chains
  108 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain L residue  129 GLU
Chi-restraints excluded: chain H residue   43 VAL
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  119 TYR
Chi-restraints excluded: chain H residue  162 THR
Chi-restraints excluded: chain H residue  165 CYS
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  204 SER
Chi-restraints excluded: chain H residue  218 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 89 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 118 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.4465 r_free = 0.4465 target = 0.114552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.094074 restraints weight = 65207.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.4035 rms_B_bonded: 5.76
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4036 r_free = 0.4036    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4036 r_free = 0.4036    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6867
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10519  Z= 0.158
  Angle     :  0.689  15.192  14284  Z= 0.346
  Chirality :  0.044   0.277   1597
  Planarity :  0.005   0.051   1813
  Dihedral  :  4.789  27.137   1410
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 20.28 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.15 (0.24), residues: 1301
  helix:  0.72 (0.26), residues: 371
  sheet:  0.19 (0.28), residues: 354
  loop : -0.76 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  15 
 TYR   0.026   0.001   TYR A 302 
 PHE   0.026   0.001   PHE B 292 
 TRP   0.022   0.002   TRP B 211 
 HIS   0.009   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (10513)
  covalent geometry    : angle       0.68857 (14272)
  SS BOND              : bond        0.00124 (    6)
  SS BOND              : angle       0.90547 (   12)
  hydrogen bonds       : bond        0.03639 (  474)
  hydrogen bonds       : angle       5.99670 ( 1336)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   86 MET cc_start: 0.4729 (tpt) cc_final: 0.4288 (tpt)
REVERT: R  155 MET cc_start: 0.7889 (ttt) cc_final: 0.7001 (ptp)
REVERT: R  214 ILE cc_start: 0.8118 (mm) cc_final: 0.7852 (mm)
REVERT: R  253 MET cc_start: 0.6394 (ttt) cc_final: 0.6061 (ttt)
REVERT: R  308 MET cc_start: 0.8419 (mmm) cc_final: 0.6943 (tpt)
REVERT: R  317 MET cc_start: 0.6651 (ppp) cc_final: 0.6306 (ppp)
REVERT: G   31 MET cc_start: 0.6175 (tmm) cc_final: 0.5403 (ttp)
REVERT: L  191 ASP cc_start: 0.7696 (t0) cc_final: 0.7344 (t0)
REVERT: H  160 MET cc_start: 0.8498 (tmm) cc_final: 0.8133 (tmm)
REVERT: H  163 LEU cc_start: 0.8361 (mt) cc_final: 0.7965 (mt)
  outliers start: 20
  outliers final: 20
  residues processed: 112
  average time/residue: 0.0900
  time to fit residues: 15.4903
Evaluate side-chains
  111 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   96 TYR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain L residue  129 GLU
Chi-restraints excluded: chain H residue   43 VAL
Chi-restraints excluded: chain H residue   92 ASN
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  119 TYR
Chi-restraints excluded: chain H residue  142 THR
Chi-restraints excluded: chain H residue  162 THR
Chi-restraints excluded: chain H residue  165 CYS
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  204 SER
Chi-restraints excluded: chain H residue  218 VAL
Chi-restraints excluded: chain H residue  228 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 113 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 111 optimal weight:    0.6980
   chunk 88 optimal weight:    7.9990
   chunk 47 optimal weight:   20.0000
   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 = 0.4471 r_free = 0.4471 target = 0.115106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.096213 restraints weight = 51894.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 5.40
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4071
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4071 r_free = 0.4071    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4070 r_free = 0.4070    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4070
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6781
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10519  Z= 0.139
  Angle     :  0.692  15.417  14284  Z= 0.343
  Chirality :  0.044   0.256   1597
  Planarity :  0.005   0.051   1813
  Dihedral  :  4.721  26.142   1410
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 20.46 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.14 (0.24), residues: 1301
  helix:  0.71 (0.26), residues: 370
  sheet:  0.23 (0.28), residues: 354
  loop : -0.75 (0.27), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  15 
 TYR   0.025   0.001   TYR A 302 
 PHE   0.027   0.001   PHE A 354 
 TRP   0.022   0.002   TRP B 211 
 HIS   0.006   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (10513)
  covalent geometry    : angle       0.69201 (14272)
  SS BOND              : bond        0.00124 (    6)
  SS BOND              : angle       0.83130 (   12)
  hydrogen bonds       : bond        0.03542 (  474)
  hydrogen bonds       : angle       5.95131 ( 1336)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   86 MET cc_start: 0.4505 (tpt) cc_final: 0.4174 (tpt)
REVERT: R  155 MET cc_start: 0.7830 (ttt) cc_final: 0.6953 (ptp)
REVERT: R  214 ILE cc_start: 0.8155 (mm) cc_final: 0.7896 (mm)
REVERT: R  253 MET cc_start: 0.6490 (ttt) cc_final: 0.6218 (ttt)
REVERT: R  308 MET cc_start: 0.8455 (mmm) cc_final: 0.7019 (tpt)
REVERT: R  317 MET cc_start: 0.6662 (ppp) cc_final: 0.6255 (ppp)
REVERT: A   10 LYS cc_start: 0.7494 (mmtt) cc_final: 0.6931 (mmmt)
REVERT: G   31 MET cc_start: 0.6370 (tmm) cc_final: 0.5840 (ttp)
REVERT: L  191 ASP cc_start: 0.7800 (t0) cc_final: 0.7400 (t0)
REVERT: H  160 MET cc_start: 0.8432 (tmm) cc_final: 0.8056 (tmm)
REVERT: H  163 LEU cc_start: 0.8257 (mt) cc_final: 0.7848 (mt)
REVERT: H  204 SER cc_start: 0.7764 (OUTLIER) cc_final: 0.7410 (p)
  outliers start: 21
  outliers final: 20
  residues processed: 111
  average time/residue: 0.0853
  time to fit residues: 14.6729
Evaluate side-chains
  112 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   96 TYR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue  129 GLU
Chi-restraints excluded: chain H residue   43 VAL
Chi-restraints excluded: chain H residue   92 ASN
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  119 TYR
Chi-restraints excluded: chain H residue  162 THR
Chi-restraints excluded: chain H residue  165 CYS
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  190 THR
Chi-restraints excluded: chain H residue  204 SER
Chi-restraints excluded: chain H residue  218 VAL
Chi-restraints excluded: chain H residue  228 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 115 optimal weight:    0.9990
   chunk 114 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 87 optimal weight:    5.9990
   chunk 121 optimal weight:    0.4980
   chunk 75 optimal weight:    0.2980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
L 180 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.115346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.093599 restraints weight = 98522.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.4022 rms_B_bonded: 7.33
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4021 r_free = 0.4021    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4021 r_free = 0.4021    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6861
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10519  Z= 0.129
  Angle     :  0.671  15.347  14284  Z= 0.334
  Chirality :  0.044   0.241   1597
  Planarity :  0.005   0.051   1813
  Dihedral  :  4.610  26.368   1410
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 20.37 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.08 (0.24), residues: 1301
  helix:  0.73 (0.26), residues: 371
  sheet:  0.25 (0.28), residues: 355
  loop : -0.68 (0.27), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 197 
 TYR   0.025   0.001   TYR A 302 
 PHE   0.025   0.001   PHE R  91 
 TRP   0.021   0.002   TRP B 211 
 HIS   0.005   0.001   HIS R 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10513)
  covalent geometry    : angle       0.67137 (14272)
  SS BOND              : bond        0.00126 (    6)
  SS BOND              : angle       0.76588 (   12)
  hydrogen bonds       : bond        0.03449 (  474)
  hydrogen bonds       : angle       5.83448 ( 1336)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2618.26 seconds
wall clock time: 45 minutes 49.44 seconds (2749.44 seconds total)