Starting phenix.real_space_refine
on Sat Aug 23 02:35:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yoo_33985/08_2025/7yoo_33985.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yoo_33985/08_2025/7yoo_33985.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yoo_33985/08_2025/7yoo_33985.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yoo_33985/08_2025/7yoo_33985.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yoo_33985/08_2025/7yoo_33985.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yoo_33985/08_2025/7yoo_33985.cif"
  }
  resolution = 3.11
  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=   0.021 sd=   0.083
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      61      5.16       5
     C    5856      2.51       5
     N    1559      2.21       5
     O    1712      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 9188
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1743
          Classifications: {'peptide': 216}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 213}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2576
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 329}
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "L"
      Number of atoms: 255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 255
          Classifications: {'peptide': 29}
          Link IDs: {'PTRANS': 3, 'TRANS': 25}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2402
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2402
          Classifications: {'peptide': 302}
          Link IDs: {'PTRANS': 10, 'TRANS': 291}
    Chain: "S"
      Number of atoms: 1794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1794
          Classifications: {'peptide': 233}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
  Time building chain proxies: 2.12, per 1000 atoms: 0.23
  Number of scatterers: 9188
  At special positions: 0
  Unit cell: (122.018, 138.006, 108.554, 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      61     16.00
     O    1712      8.00
     N    1559      7.00
     C    5856      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 123 " - pdb=" SG  CYS R 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " 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: 0.83
  Conformation dependent library (CDL) restraints added in 366.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2192

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 15 sheets defined
      37.8% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 28
      removed outlier: 3.582A  pdb=" N   VAL A  13 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLU A  14 " --> pdb=" O   LYS A  10 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ARG A  15 " --> pdb=" O   ALA A  11 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLU A  28 " --> pdb=" O   ARG A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 33
      removed outlier: 4.052A  pdb=" N   GLU A  33 " --> pdb=" O   ALA A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 54
      removed outlier: 3.647A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LYS A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.030A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
      removed outlier: 3.500A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 213 through 216'
    Processing helix  chain 'A' and resid 242 through 255
      removed outlier: 3.747A  pdb=" N   SER A 246 " --> pdb=" O   ARG A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.624A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.616A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   PHE A 307 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 351
      removed outlier: 3.557A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU A 348 " --> pdb=" O   ILE A 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 26
      removed outlier: 3.531A  pdb=" N   ARG B  19 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA B  24 " --> pdb=" O   ASP B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 12 through 24
      removed outlier: 4.026A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLN G  18 " --> pdb=" O   LYS G  14 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU G  19 " --> pdb=" O   LEU G  15 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLU G  22 " --> pdb=" O   GLN G  18 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.744A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLU G  42 " --> pdb=" O   MET G  38 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'L' and resid 17 through 32
    Processing helix  chain 'R' and resid 42 through 45
    Processing helix  chain 'R' and resid 46 through 78
      removed outlier: 3.614A  pdb=" N   VAL R  52 " --> pdb=" O   GLU R  48 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU R  70 " --> pdb=" O   ILE R  66 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL R  71 " --> pdb=" O   GLY R  67 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ILE R  72 " --> pdb=" O   ASN R  68 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 83 through 113
      removed outlier: 3.530A  pdb=" N   PHE R  88 " --> pdb=" O   VAL R  84 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ILE R  89 " --> pdb=" O   THR R  85 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   LEU R 104 " --> pdb=" O   ASN R 100 " (cutoff:3.500A)
      Proline residue:  R 105  - end of helix
    Processing helix  chain 'R' and resid 119 through 124
      removed outlier: 4.032A  pdb=" N   HIS R 124 " --> pdb=" O   PRO R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 125 through 153
      removed outlier: 3.960A  pdb=" N   VAL R 134 " --> pdb=" O   GLN R 130 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLN R 135 " --> pdb=" O   GLY R 131 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   THR R 142 " --> pdb=" O   THR R 138 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 161 through 180
      removed outlier: 3.519A  pdb=" N   TRP R 173 " --> pdb=" O   ILE R 169 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU R 178 " --> pdb=" O   GLY R 174 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 180 through 186
      removed outlier: 4.183A  pdb=" N   ALA R 184 " --> pdb=" O   ALA R 180 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 213 through 228
      removed outlier: 4.264A  pdb=" N   THR R 217 " --> pdb=" O   SER R 213 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   TYR R 219 " --> pdb=" O   TYR R 215 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   SER R 220 " --> pdb=" O   GLY R 216 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU R 221 " --> pdb=" O   THR R 217 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU R 225 " --> pdb=" O   LEU R 221 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 228 through 248
      removed outlier: 3.576A  pdb=" N   LEU R 232 " --> pdb=" O   TYR R 228 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 255 through 281
      removed outlier: 3.542A  pdb=" N   TYR R 259 " --> pdb=" O   ALA R 255 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLN R 264 " --> pdb=" O   HIS R 260 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   LYS R 265 " --> pdb=" O   GLN R 261 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   THR R 266 " --> pdb=" O   ARG R 262 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   THR R 267 " --> pdb=" O   ARG R 263 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LYS R 268 " --> pdb=" O   GLN R 264 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   MET R 269 " --> pdb=" O   LYS R 265 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL R 273 " --> pdb=" O   MET R 269 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL R 274 " --> pdb=" O   LEU R 270 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   PHE R 277 " --> pdb=" O   VAL R 273 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   TRP R 281 " --> pdb=" O   PHE R 277 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 281 through 294
    Processing helix  chain 'R' and resid 302 through 315
    Processing helix  chain 'R' and resid 316 through 319
    Processing helix  chain 'R' and resid 320 through 325
    Processing helix  chain 'R' and resid 329 through 341
      removed outlier: 4.005A  pdb=" N   LYS R 334 " --> pdb=" O   SER R 330 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ALA R 335 " --> pdb=" O   ASN R 331 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.525A  pdb=" N   SER S  31 " --> pdb=" O   ALA S  28 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.976A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.612A  pdb=" N   LEU A  38 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.914A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 9.298A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.531A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.020A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.868A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.576A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.812A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.143A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.655A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.247A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.846A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 188 through 195
      removed outlier: 4.061A  pdb=" N   SER R 190 " --> pdb=" O   ALA R 202 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   PHE R 198 " --> pdb=" O   ILE R 194 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.641A  pdb=" N   PHE S  80 " --> pdb=" O   SER S  71 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   SER S  71 " --> pdb=" O   PHE S  80 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12
    Processing sheet with id=AB4, first strand: chain 'S' and resid 58 through 60
      removed outlier: 6.603A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   TYR S  94 " --> pdb=" O   THR S 115 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   THR S 115 " --> pdb=" O   TYR S  94 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 158 through 159
      removed outlier: 3.992A  pdb=" N   ALA S 211 " --> pdb=" O   SER S 208 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195
      removed outlier: 5.635A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)

    378 hydrogen bonds defined for protein.
    1071 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: 1.55

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1484
        1.31 -     1.44: 2578
        1.44 -     1.57: 5229
        1.57 -     1.70: 0
        1.70 -     1.83: 88
  Bond restraints: 9379
  Sorted by residual:
  bond pdb=" C   TYC L  36 "
       pdb=" NXT TYC L  36 "
    ideal  model  delta    sigma   weight residual
    1.340  1.450 -0.110 2.00e-02 2.50e+03 3.05e+01
  bond pdb=" CZ  TYC L  36 "
       pdb=" OH  TYC L  36 "
    ideal  model  delta    sigma   weight residual
    1.350  1.398 -0.048 2.00e-02 2.50e+03 5.74e+00
  bond pdb=" C   TYC L  36 "
       pdb=" O   TYC L  36 "
    ideal  model  delta    sigma   weight residual
    1.231  1.184  0.047 2.00e-02 2.50e+03 5.51e+00
  bond pdb=" CB  TYC L  36 "
       pdb=" CG  TYC L  36 "
    ideal  model  delta    sigma   weight residual
    1.501  1.526 -0.025 2.00e-02 2.50e+03 1.51e+00
  bond pdb=" C   LEU R 104 "
       pdb=" N   PRO R 105 "
    ideal  model  delta    sigma   weight residual
    1.336  1.350 -0.014 1.20e-02 6.94e+03 1.36e+00
  ... (remaining 9374 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 12389
        1.14 -     2.27: 242
        2.27 -     3.41: 52
        3.41 -     4.54: 10
        4.54 -     5.68: 9
  Bond angle restraints: 12702
  Sorted by residual:
  angle pdb=" CA  GLY B 216 "
        pdb=" C   GLY B 216 "
        pdb=" N   MET B 217 "
      ideal   model   delta    sigma   weight residual
     118.67  115.93    2.74 9.80e-01 1.04e+00 7.82e+00
  angle pdb=" C   ARG S 191 "
        pdb=" N   MET S 192 "
        pdb=" CA  MET S 192 "
      ideal   model   delta    sigma   weight residual
     121.54  126.69   -5.15 1.91e+00 2.74e-01 7.26e+00
  angle pdb=" N   GLY B 216 "
        pdb=" CA  GLY B 216 "
        pdb=" C   GLY B 216 "
      ideal   model   delta    sigma   weight residual
     116.01  111.60    4.41 1.64e+00 3.72e-01 7.24e+00
  angle pdb=" CA  GLY B 216 "
        pdb=" C   GLY B 216 "
        pdb=" O   GLY B 216 "
      ideal   model   delta    sigma   weight residual
     118.77  121.05   -2.28 9.40e-01 1.13e+00 5.90e+00
  angle pdb=" CA  CYS B 149 "
        pdb=" CB  CYS B 149 "
        pdb=" SG  CYS B 149 "
      ideal   model   delta    sigma   weight residual
     114.40  118.73   -4.33 2.30e+00 1.89e-01 3.54e+00
  ... (remaining 12697 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 5075
       17.75 -    35.50: 409
       35.50 -    53.26: 90
       53.26 -    71.01: 12
       71.01 -    88.76: 3
  Dihedral angle restraints: 5589
    sinusoidal: 2191
      harmonic: 3398
  Sorted by residual:
  dihedral pdb=" CG  ARG B  52 "
           pdb=" CD  ARG B  52 "
           pdb=" NE  ARG B  52 "
           pdb=" CZ  ARG B  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.10  -44.90     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CG  ARG S  98 "
           pdb=" CD  ARG S  98 "
           pdb=" NE  ARG S  98 "
           pdb=" CZ  ARG S  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  139.00   41.00     2      1.50e+01 4.44e-03 9.18e+00
  dihedral pdb=" CB  LYS R 117 "
           pdb=" CG  LYS R 117 "
           pdb=" CD  LYS R 117 "
           pdb=" CE  LYS R 117 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -112.40   52.40     3      1.50e+01 4.44e-03 9.11e+00
  ... (remaining 5586 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 905
       0.029 -    0.059: 372
       0.059 -    0.088: 93
       0.088 -    0.118: 66
       0.118 -    0.147: 10
  Chirality restraints: 1446
  Sorted by residual:
  chirality pdb=" CA  ILE R 195 "
            pdb=" N   ILE R 195 "
            pdb=" C   ILE R 195 "
            pdb=" CB  ILE R 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.40e-01
  chirality pdb=" CB  VAL A 201 "
            pdb=" CA  VAL A 201 "
            pdb=" CG1 VAL A 201 "
            pdb=" CG2 VAL A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.32e-01
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.01e-01
  ... (remaining 1443 not shown)

  Planarity restraints: 1598
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 287 "   -0.053 5.00e-02 4.00e+02   8.01e-02 1.03e+01
        pdb=" N   PRO A 288 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A 288 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 288 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 193 "   -0.008 2.00e-02 2.50e+03   1.57e-02 2.45e+00
        pdb=" CG  ASP A 193 "    0.027 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 193 "   -0.010 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 193 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 195 "   -0.024 5.00e-02 4.00e+02   3.72e-02 2.21e+00
        pdb=" N   PRO R 196 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO R 196 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO R 196 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1595 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 175
        2.70 -     3.25: 8642
        3.25 -     3.80: 13260
        3.80 -     4.35: 17677
        4.35 -     4.90: 30775
  Nonbonded interactions: 70529
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" O   GLY A  40 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" NH2 ARG S  67 "
            pdb=" OD2 ASP S  90 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" OG  SER S  17 "
            pdb=" O   MET S  83 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASP B 154 "
     model   vdw
     2.334 3.040
  ... (remaining 70524 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.890
  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:             0.020
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     9.170
  Find NCS groups from input model:        0.060
  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:             0.010
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
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      :  0.003   0.110   9383  Z= 0.115
  Angle     :  0.437   5.675  12710  Z= 0.229
  Chirality :  0.039   0.147   1446
  Planarity :  0.003   0.080   1598
  Dihedral  : 13.434  88.762   3385
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.25), residues: 1148
  helix: -0.06 (0.27), residues: 370
  sheet:  0.37 (0.34), residues: 251
  loop : -0.23 (0.27), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 150 
 TYR   0.009   0.001   TYR S 190 
 PHE   0.008   0.001   PHE B 199 
 TRP   0.007   0.001   TRP S  47 
 HIS   0.004   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 9379)
  covalent geometry    : angle       0.43628 (12702)
  SS BOND              : bond        0.00602 (    4)
  SS BOND              : angle       1.31207 (    8)
  hydrogen bonds       : bond        0.29549 (  370)
  hydrogen bonds       : angle       7.53239 ( 1071)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A  246 SER cc_start: 0.7112 (p) cc_final: 0.6875 (p)
REVERT: A  305 CYS cc_start: 0.7607 (m) cc_final: 0.7299 (m)
REVERT: R  315 MET cc_start: 0.7175 (mmt) cc_final: 0.6875 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.1246
  time to fit residues: 24.7876
Evaluate side-chains
  128 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
** R  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 100 ASN
S 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.119496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.094408 restraints weight = 16233.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.79
r_work: 0.3098 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9383  Z= 0.156
  Angle     :  0.537   6.607  12710  Z= 0.286
  Chirality :  0.042   0.164   1446
  Planarity :  0.004   0.058   1598
  Dihedral  :  4.876  56.287   1273
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  8.14 %
    Favored  : 90.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.34 (0.25), residues: 1148
  helix:  0.94 (0.27), residues: 377
  sheet:  0.22 (0.31), residues: 287
  loop : -0.21 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 241 
 TYR   0.013   0.001   TYR S 190 
 PHE   0.012   0.001   PHE S  29 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 9379)
  covalent geometry    : angle       0.53436 (12702)
  SS BOND              : bond        0.01090 (    4)
  SS BOND              : angle       2.08864 (    8)
  hydrogen bonds       : bond        0.06162 (  370)
  hydrogen bonds       : angle       4.65058 ( 1071)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  305 CYS cc_start: 0.7624 (m) cc_final: 0.7248 (m)
REVERT: B   17 GLN cc_start: 0.6935 (tm-30) cc_final: 0.6570 (tm-30)
REVERT: B  258 ASP cc_start: 0.6962 (t0) cc_final: 0.6280 (t70)
REVERT: R  188 GLU cc_start: 0.7533 (pp20) cc_final: 0.7147 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 145
  average time/residue: 0.1276
  time to fit residues: 24.2099
Evaluate side-chains
  133 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain S residue  168 SER
Chi-restraints excluded: chain S residue  186 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 25 optimal weight:    0.4980
   chunk 107 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 97 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 306 GLN
** R  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.119925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.090966 restraints weight = 16281.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.72
r_work: 0.3097 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9383  Z= 0.132
  Angle     :  0.492   5.900  12710  Z= 0.262
  Chirality :  0.041   0.164   1446
  Planarity :  0.003   0.050   1598
  Dihedral  :  4.567  48.706   1273
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  9.83 %
    Favored  : 88.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.25), residues: 1148
  helix:  1.22 (0.27), residues: 380
  sheet:  0.24 (0.30), residues: 286
  loop : -0.24 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 241 
 TYR   0.014   0.001   TYR S 190 
 PHE   0.028   0.001   PHE R 319 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9379)
  covalent geometry    : angle       0.49049 (12702)
  SS BOND              : bond        0.00990 (    4)
  SS BOND              : angle       1.79238 (    8)
  hydrogen bonds       : bond        0.04956 (  370)
  hydrogen bonds       : angle       4.21951 ( 1071)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.444 
Fit side-chains
REVERT: A   53 MET cc_start: 0.7476 (mmt) cc_final: 0.7234 (mmt)
REVERT: A  305 CYS cc_start: 0.7589 (m) cc_final: 0.7224 (m)
REVERT: B   18 ILE cc_start: 0.7158 (mm) cc_final: 0.6899 (mt)
REVERT: B  150 ARG cc_start: 0.7970 (ttm-80) cc_final: 0.7746 (ttm-80)
REVERT: B  258 ASP cc_start: 0.7109 (t0) cc_final: 0.6556 (t70)
REVERT: B  335 PHE cc_start: 0.8721 (m-80) cc_final: 0.8514 (m-80)
REVERT: R  135 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8025 (mt0)
REVERT: R  188 GLU cc_start: 0.7485 (pp20) cc_final: 0.7069 (tm-30)
REVERT: R  291 VAL cc_start: 0.8023 (t) cc_final: 0.7721 (p)
  outliers start: 15
  outliers final: 10
  residues processed: 137
  average time/residue: 0.1269
  time to fit residues: 22.5990
Evaluate side-chains
  139 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain R residue  135 GLN
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  214 ILE
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  168 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 8 optimal weight:    0.1980
   chunk 46 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 52 optimal weight:    0.1980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 306 GLN
** R  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.120061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.090592 restraints weight = 16237.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.75
r_work: 0.3088 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9383  Z= 0.113
  Angle     :  0.468   5.279  12710  Z= 0.249
  Chirality :  0.041   0.168   1446
  Planarity :  0.003   0.044   1598
  Dihedral  :  4.198  39.029   1273
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 11.92 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.25), residues: 1148
  helix:  1.38 (0.27), residues: 385
  sheet:  0.21 (0.30), residues: 281
  loop : -0.30 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  46 
 TYR   0.014   0.001   TYR S 190 
 PHE   0.036   0.001   PHE R 319 
 TRP   0.011   0.001   TRP B 211 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9379)
  covalent geometry    : angle       0.46617 (12702)
  SS BOND              : bond        0.00872 (    4)
  SS BOND              : angle       1.59339 (    8)
  hydrogen bonds       : bond        0.04188 (  370)
  hydrogen bonds       : angle       3.97572 ( 1071)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 136
  time to evaluate  : 0.416 
Fit side-chains
REVERT: A   51 LYS cc_start: 0.7867 (pttp) cc_final: 0.7452 (ptmm)
REVERT: A  305 CYS cc_start: 0.7369 (m) cc_final: 0.6988 (m)
REVERT: B  258 ASP cc_start: 0.7124 (t0) cc_final: 0.6609 (t70)
REVERT: B  335 PHE cc_start: 0.8691 (m-80) cc_final: 0.8415 (m-80)
REVERT: R  135 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7994 (mt0)
REVERT: R  291 VAL cc_start: 0.7938 (t) cc_final: 0.7654 (p)
  outliers start: 15
  outliers final: 11
  residues processed: 142
  average time/residue: 0.1381
  time to fit residues: 25.3350
Evaluate side-chains
  140 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain R residue  135 GLN
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  269 MET
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  168 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0670
   chunk 52 optimal weight:    0.3980
   chunk 107 optimal weight:    0.9990
   chunk 102 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0470
   chunk 109 optimal weight:    0.0010
   chunk 8 optimal weight:    0.0670
   chunk 106 optimal weight:    0.4980
   chunk 54 optimal weight:    0.0060
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.0376

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 306 GLN
A 331 ASN
S  39 GLN
S 179 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.124279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.095079 restraints weight = 16314.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 2.75
r_work: 0.3159 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9383  Z= 0.081
  Angle     :  0.417   5.057  12710  Z= 0.224
  Chirality :  0.039   0.169   1446
  Planarity :  0.003   0.046   1598
  Dihedral  :  3.668  28.006   1273
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.61 %
    Favored  : 86.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.25), residues: 1148
  helix:  1.56 (0.27), residues: 391
  sheet:  0.32 (0.31), residues: 275
  loop : -0.19 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 150 
 TYR   0.016   0.001   TYR S 190 
 PHE   0.028   0.001   PHE R 319 
 TRP   0.011   0.001   TRP S  47 
 HIS   0.004   0.001   HIS R 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00163 ( 9379)
  covalent geometry    : angle       0.41691 (12702)
  SS BOND              : bond        0.00348 (    4)
  SS BOND              : angle       0.86626 (    8)
  hydrogen bonds       : bond        0.03115 (  370)
  hydrogen bonds       : angle       3.69042 ( 1071)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 141
  time to evaluate  : 0.451 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.7062 (t0) cc_final: 0.6575 (t70)
REVERT: B  266 HIS cc_start: 0.7811 (OUTLIER) cc_final: 0.7335 (t-90)
REVERT: R  135 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7997 (mt0)
REVERT: R  214 ILE cc_start: 0.8064 (tp) cc_final: 0.7791 (pt)
REVERT: R  291 VAL cc_start: 0.7920 (t) cc_final: 0.7654 (p)
  outliers start: 13
  outliers final: 8
  residues processed: 148
  average time/residue: 0.1367
  time to fit residues: 26.2133
Evaluate side-chains
  148 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 138
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain R residue  135 GLN
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  109 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 40 optimal weight:    0.0040
   chunk 86 optimal weight:    0.9980
   chunk 92 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   chunk 111 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 306 GLN
A 311 ASN
A 331 ASN
** R  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 258 HIS
S 179 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.119783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.091959 restraints weight = 16209.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.87
r_work: 0.3083 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9383  Z= 0.128
  Angle     :  0.481   5.498  12710  Z= 0.254
  Chirality :  0.041   0.173   1446
  Planarity :  0.003   0.047   1598
  Dihedral  :  3.660  18.111   1273
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.61 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.25), residues: 1148
  helix:  1.57 (0.27), residues: 393
  sheet:  0.23 (0.30), residues: 287
  loop : -0.25 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 241 
 TYR   0.011   0.001   TYR S 190 
 PHE   0.026   0.001   PHE R 319 
 TRP   0.011   0.001   TRP B 211 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9379)
  covalent geometry    : angle       0.47925 (12702)
  SS BOND              : bond        0.00922 (    4)
  SS BOND              : angle       1.57980 (    8)
  hydrogen bonds       : bond        0.03964 (  370)
  hydrogen bonds       : angle       3.77089 ( 1071)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.331 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.7112 (t0) cc_final: 0.6606 (t70)
REVERT: B  266 HIS cc_start: 0.7839 (OUTLIER) cc_final: 0.7318 (t-90)
REVERT: R  135 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8055 (mt0)
REVERT: R  214 ILE cc_start: 0.8034 (tp) cc_final: 0.7747 (pt)
REVERT: R  291 VAL cc_start: 0.7903 (t) cc_final: 0.7646 (p)
REVERT: S  116 THR cc_start: 0.8664 (p) cc_final: 0.8421 (t)
  outliers start: 17
  outliers final: 10
  residues processed: 147
  average time/residue: 0.1348
  time to fit residues: 25.4340
Evaluate side-chains
  148 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain R residue  135 GLN
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  109 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 112 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 306 GLN
R 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.119871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.089808 restraints weight = 16314.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.81
r_work: 0.3070 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9383  Z= 0.135
  Angle     :  0.496   7.335  12710  Z= 0.261
  Chirality :  0.041   0.171   1446
  Planarity :  0.003   0.048   1598
  Dihedral  :  3.721  18.174   1273
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.41 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.25), residues: 1148
  helix:  1.55 (0.27), residues: 393
  sheet:  0.20 (0.30), residues: 285
  loop : -0.28 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 241 
 TYR   0.012   0.001   TYR B  59 
 PHE   0.025   0.001   PHE R 319 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 9379)
  covalent geometry    : angle       0.49410 (12702)
  SS BOND              : bond        0.00988 (    4)
  SS BOND              : angle       1.71903 (    8)
  hydrogen bonds       : bond        0.04152 (  370)
  hydrogen bonds       : angle       3.81212 ( 1071)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A   51 LYS cc_start: 0.7866 (pttp) cc_final: 0.7487 (ptmm)
REVERT: B  258 ASP cc_start: 0.7078 (t0) cc_final: 0.6590 (t70)
REVERT: B  266 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7378 (t-90)
REVERT: R   45 LYS cc_start: 0.7336 (tptt) cc_final: 0.7014 (tmtt)
REVERT: R  135 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8055 (mt0)
REVERT: R  214 ILE cc_start: 0.8026 (tp) cc_final: 0.7722 (pt)
REVERT: R  291 VAL cc_start: 0.7914 (t) cc_final: 0.7646 (p)
REVERT: S   19 LYS cc_start: 0.8864 (tttm) cc_final: 0.8653 (tttm)
REVERT: S  116 THR cc_start: 0.8730 (p) cc_final: 0.8499 (t)
  outliers start: 19
  outliers final: 12
  residues processed: 148
  average time/residue: 0.1336
  time to fit residues: 25.5135
Evaluate side-chains
  148 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 134
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue  135 GLN
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  269 MET
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  109 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 91 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 108 optimal weight:    0.0970
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 306 GLN
R 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.120361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.090398 restraints weight = 16189.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.79
r_work: 0.3083 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9383  Z= 0.121
  Angle     :  0.482   6.919  12710  Z= 0.256
  Chirality :  0.041   0.171   1446
  Planarity :  0.003   0.047   1598
  Dihedral  :  3.680  17.930   1273
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.50 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.25), residues: 1148
  helix:  1.65 (0.27), residues: 393
  sheet:  0.20 (0.30), residues: 283
  loop : -0.31 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 241 
 TYR   0.013   0.001   TYR S 190 
 PHE   0.036   0.001   PHE R 319 
 TRP   0.011   0.001   TRP B 211 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9379)
  covalent geometry    : angle       0.48067 (12702)
  SS BOND              : bond        0.00860 (    4)
  SS BOND              : angle       1.70514 (    8)
  hydrogen bonds       : bond        0.03951 (  370)
  hydrogen bonds       : angle       3.75302 ( 1071)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A   51 LYS cc_start: 0.7871 (pttp) cc_final: 0.7493 (ptmm)
REVERT: B  258 ASP cc_start: 0.7068 (t0) cc_final: 0.6592 (t70)
REVERT: B  266 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7363 (t-90)
REVERT: R  135 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8073 (mt0)
REVERT: R  188 GLU cc_start: 0.7629 (pp20) cc_final: 0.7106 (tm-30)
REVERT: R  214 ILE cc_start: 0.8010 (tp) cc_final: 0.7710 (pt)
REVERT: R  291 VAL cc_start: 0.7898 (t) cc_final: 0.7630 (p)
  outliers start: 19
  outliers final: 16
  residues processed: 153
  average time/residue: 0.1226
  time to fit residues: 24.0527
Evaluate side-chains
  156 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain R residue   61 ILE
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue  135 GLN
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  266 THR
Chi-restraints excluded: chain R residue  269 MET
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  109 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 73 optimal weight:    0.3980
   chunk 105 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 306 GLN
R 258 HIS
R 261 GLN
S  82 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.120153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.090505 restraints weight = 16195.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.75
r_work: 0.3070 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9383  Z= 0.147
  Angle     :  0.516   7.132  12710  Z= 0.273
  Chirality :  0.042   0.171   1446
  Planarity :  0.003   0.047   1598
  Dihedral  :  3.784  17.962   1273
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 14.70 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.25), residues: 1148
  helix:  1.71 (0.27), residues: 387
  sheet:  0.23 (0.30), residues: 283
  loop : -0.34 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 241 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.034   0.001   PHE R 319 
 TRP   0.011   0.001   TRP B 211 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9379)
  covalent geometry    : angle       0.51428 (12702)
  SS BOND              : bond        0.01056 (    4)
  SS BOND              : angle       1.86894 (    8)
  hydrogen bonds       : bond        0.04243 (  370)
  hydrogen bonds       : angle       3.82671 ( 1071)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A   51 LYS cc_start: 0.7884 (pttp) cc_final: 0.7506 (ptmm)
REVERT: B  153 ASP cc_start: 0.7837 (t0) cc_final: 0.7547 (t0)
REVERT: B  258 ASP cc_start: 0.7047 (t0) cc_final: 0.6579 (t70)
REVERT: B  266 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7360 (t-90)
REVERT: R  135 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8072 (mt0)
REVERT: R  188 GLU cc_start: 0.7776 (pp20) cc_final: 0.7294 (tm-30)
REVERT: R  291 VAL cc_start: 0.7970 (t) cc_final: 0.7698 (p)
  outliers start: 21
  outliers final: 16
  residues processed: 147
  average time/residue: 0.1319
  time to fit residues: 24.9130
Evaluate side-chains
  152 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain R residue   61 ILE
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue  135 GLN
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  266 THR
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  168 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 94 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0010
   chunk 63 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 32 optimal weight:    0.3980
   chunk 88 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 306 GLN
G  59 ASN
R 258 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.120425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.091582 restraints weight = 16210.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.72
r_work: 0.3089 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9383  Z= 0.113
  Angle     :  0.480   6.700  12710  Z= 0.255
  Chirality :  0.041   0.170   1446
  Planarity :  0.003   0.048   1598
  Dihedral  :  3.673  18.050   1273
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.19 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.25), residues: 1148
  helix:  1.78 (0.27), residues: 387
  sheet:  0.21 (0.30), residues: 281
  loop : -0.29 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 241 
 TYR   0.014   0.001   TYR S 190 
 PHE   0.033   0.001   PHE R 319 
 TRP   0.011   0.001   TRP B 211 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9379)
  covalent geometry    : angle       0.47838 (12702)
  SS BOND              : bond        0.00817 (    4)
  SS BOND              : angle       1.55408 (    8)
  hydrogen bonds       : bond        0.03797 (  370)
  hydrogen bonds       : angle       3.74378 ( 1071)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A   51 LYS cc_start: 0.7850 (pttp) cc_final: 0.7486 (ptmm)
REVERT: B  153 ASP cc_start: 0.7820 (t0) cc_final: 0.7570 (t0)
REVERT: B  258 ASP cc_start: 0.7041 (t0) cc_final: 0.6585 (t70)
REVERT: B  266 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.7593 (t-90)
REVERT: R  135 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8076 (mt0)
REVERT: R  291 VAL cc_start: 0.7915 (t) cc_final: 0.7632 (p)
  outliers start: 18
  outliers final: 16
  residues processed: 149
  average time/residue: 0.1282
  time to fit residues: 24.6306
Evaluate side-chains
  153 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain G residue   59 ASN
Chi-restraints excluded: chain R residue   61 ILE
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue  135 GLN
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  266 THR
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  109 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 71 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0970
   chunk 72 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0970
   chunk 2 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0170
   chunk 113 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0870
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.1792

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 306 GLN
R 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.122179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.092715 restraints weight = 16048.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 2.71
r_work: 0.3115 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9383  Z= 0.094
  Angle     :  0.467   5.963  12710  Z= 0.251
  Chirality :  0.040   0.175   1446
  Planarity :  0.003   0.048   1598
  Dihedral  :  3.616  17.786   1273
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 15.29 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.25), residues: 1148
  helix:  1.79 (0.27), residues: 393
  sheet:  0.27 (0.30), residues: 276
  loop : -0.32 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 241 
 TYR   0.016   0.001   TYR S 190 
 PHE   0.033   0.001   PHE R 319 
 TRP   0.011   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 9379)
  covalent geometry    : angle       0.46603 (12702)
  SS BOND              : bond        0.00625 (    4)
  SS BOND              : angle       1.30615 (    8)
  hydrogen bonds       : bond        0.03543 (  370)
  hydrogen bonds       : angle       3.71214 ( 1071)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2721.11 seconds
wall clock time: 47 minutes 14.54 seconds (2834.54 seconds total)