Starting phenix.real_space_refine
on Thu Feb 13 03:19:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6n4b_0339/02_2025/6n4b_0339_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6n4b_0339/02_2025/6n4b_0339.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6n4b_0339/02_2025/6n4b_0339.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6n4b_0339/02_2025/6n4b_0339.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6n4b_0339/02_2025/6n4b_0339_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6n4b_0339/02_2025/6n4b_0339_neut.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    5423      2.51       5
     N    1457      2.21       5
     O    1514      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8453
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1646
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 131
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 72
    Chain: "B"
      Number of atoms: 2553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2553
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 435
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 1988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 1988
          Classifications: {'peptide': 276}
          Incomplete info: {'truncation_to_alanine': 71}
          Link IDs: {'PTRANS': 8, 'TRANS': 267}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 215
          Unresolved non-hydrogen angles: 269
          Unresolved non-hydrogen dihedrals: 167
          Unresolved non-hydrogen chiralities: 29
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 88
    Chain: "S"
      Number of atoms: 1746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1746
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 85
          Unusual residues: {'CLR': 2}
          Classifications: {'peptide': 1, 'undetermined': 2}
          Link IDs: {None: 2}
  Time building chain proxies: 5.39, per 1000 atoms: 0.64
  Number of scatterers: 8453
  At special positions: 0
  Unit cell: (109.22, 122.98, 109.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      58     16.00
     F       1      9.00
     O    1514      8.00
     N    1457      7.00
     C    5423      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 257 " - pdb=" SG  CYS R 264 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.62
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2100

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      35.1% alpha, 20.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 28
      removed outlier: 3.718A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ARG A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 51
      removed outlier: 3.937A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.453A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
      removed outlier: 4.060A  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 241 through 255
      removed outlier: 3.911A  pdb=" N   GLU A 245 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.665A  pdb=" N   PHE A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ILE A 278 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.509A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.577A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   TYR A 302 " --> pdb=" O   GLU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.506A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   THR A 340 " --> pdb=" O   PHE A 336 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   LYS A 349 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   CYS A 351 " --> pdb=" O   ASN A 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 18
      removed outlier: 3.550A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.803A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 22
      removed outlier: 3.622A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU C  22 " --> pdb=" O   GLN C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'C' and resid 34 through 39
    Processing helix  chain 'R' and resid 112 through 143
      removed outlier: 4.519A  pdb=" N   VAL R 121 " --> pdb=" O   LEU R 117 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU R 122 " --> pdb=" O   ALA R 118 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER R 123 " --> pdb=" O   ILE R 119 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   VAL R 140 " --> pdb=" O   LEU R 136 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE R 141 " --> pdb=" O   VAL R 137 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 151 through 179
      removed outlier: 3.937A  pdb=" N   PHE R 155 " --> pdb=" O   PRO R 151 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ILE R 156 " --> pdb=" O   SER R 152 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA R 162 " --> pdb=" O   SER R 158 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU R 164 " --> pdb=" O   ALA R 160 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TYR R 172 " --> pdb=" O   VAL R 168 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL R 179 " --> pdb=" O   ILE R 175 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 185 through 191
      removed outlier: 4.288A  pdb=" N   LEU R 190 " --> pdb=" O   ARG R 186 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   PHE R 191 " --> pdb=" O   ASN R 187 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 193 through 212
      removed outlier: 3.622A  pdb=" N   ILE R 212 " --> pdb=" O   PHE R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 212 through 220
      removed outlier: 3.632A  pdb=" N   ILE R 216 " --> pdb=" O   ILE R 212 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   ILE R 218 " --> pdb=" O   ARG R 214 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 220 through 228
      removed outlier: 4.523A  pdb=" N   LYS R 225 " --> pdb=" O   PRO R 221 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   ARG R 226 " --> pdb=" O   LEU R 222 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL R 228 " --> pdb=" O   TYR R 224 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 229 through 249
    Processing helix  chain 'R' and resid 249 through 254
      removed outlier: 4.183A  pdb=" N   LEU R 253 " --> pdb=" O   VAL R 249 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 272 through 277
    Processing helix  chain 'R' and resid 278 through 311
      removed outlier: 3.693A  pdb=" N   VAL R 282 " --> pdb=" O   PHE R 278 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ILE R 290 " --> pdb=" O   LEU R 286 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   MET R 295 " --> pdb=" O   VAL R 291 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ILE R 297 " --> pdb=" O   ALA R 293 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE R 309 " --> pdb=" O   ALA R 305 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 336 through 355
      removed outlier: 3.842A  pdb=" N   ALA R 342 " --> pdb=" O   ASP R 338 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS R 343 " --> pdb=" O   ILE R 339 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   THR R 344 " --> pdb=" O   ARG R 340 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU R 347 " --> pdb=" O   LYS R 343 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL R 351 " --> pdb=" O   LEU R 347 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE R 353 " --> pdb=" O   LEU R 349 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 358 through 363
    Processing helix  chain 'R' and resid 374 through 399
      removed outlier: 3.708A  pdb=" N   ALA R 380 " --> pdb=" O   LYS R 376 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   PHE R 381 " --> pdb=" O   THR R 377 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   MET R 384 " --> pdb=" O   ALA R 380 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU R 385 " --> pdb=" O   PHE R 381 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   CYS R 386 " --> pdb=" O   CYS R 382 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LEU R 387 " --> pdb=" O   SER R 383 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU R 388 " --> pdb=" O   MET R 384 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   SER R 390 " --> pdb=" O   CYS R 386 " (cutoff:3.500A)
      Proline residue:  R 394  - end of helix
    Processing helix  chain 'R' and resid 401 through 410
      removed outlier: 3.514A  pdb=" N   ARG R 405 " --> pdb=" O   SER R 401 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.707A  pdb=" N   SER S  31 " --> pdb=" O   ALA S  28 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   PHE S  32 " --> pdb=" O   PHE S  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 28 through 32'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 7.273A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.246A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 9.070A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.601A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA B 328 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.918A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.568A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 4.012A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU B 152 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.969A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.730A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.765A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.775A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7
      removed outlier: 3.660A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.391A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   THR S 115 " --> pdb=" O   TYR S  94 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU S 117 " --> pdb=" O   ALA S  92 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA S  92 " --> pdb=" O   LEU S 117 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   TRP S  36 " --> pdb=" O   ALA S  49 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.391A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   THR S 115 " --> pdb=" O   TYR S  94 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU S 117 " --> pdb=" O   ALA S  92 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA S  92 " --> pdb=" O   LEU S 117 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB4, first strand: chain 'S' and resid 135 through 136
      removed outlier: 6.100A  pdb=" N   VAL S 135 " --> pdb=" O   GLU S 234 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'S' and resid 174 through 177
      removed outlier: 6.658A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    325 hydrogen bonds defined for protein.
    936 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.55

  Time building geometry restraints manager: 2.81 seconds

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

  Histogram of bond lengths:
        1.10 -     1.24: 1206
        1.24 -     1.39: 2297
        1.39 -     1.53: 4598
        1.53 -     1.67: 451
        1.67 -     1.81: 84
  Bond restraints: 8636
  Sorted by residual:
  bond pdb=" CAT KCA R 501 "
       pdb=" FAU KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.342  1.101  0.241 2.00e-02 2.50e+03 1.45e+02
  bond pdb=" CAB KCA R 501 "
       pdb=" CAM KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.476  1.351  0.125 2.00e-02 2.50e+03 3.91e+01
  bond pdb=" CA  TRP B 339 "
       pdb=" C   TRP B 339 "
    ideal  model  delta    sigma   weight residual
    1.523  1.457  0.067 1.18e-02 7.18e+03 3.19e+01
  bond pdb=" CAP KCA R 501 "
       pdb=" CAQ KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.507  1.395  0.112 2.00e-02 2.50e+03 3.12e+01
  bond pdb=" CA  LEU B 336 "
       pdb=" C   LEU B 336 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 1.19e-02 7.06e+03 2.07e+01
  ... (remaining 8631 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.46: 11350
        3.46 -     6.92: 352
        6.92 -    10.39: 39
       10.39 -    13.85: 6
       13.85 -    17.31: 1
  Bond angle restraints: 11748
  Sorted by residual:
  angle pdb=" N   PHE R 177 "
        pdb=" CA  PHE R 177 "
        pdb=" C   PHE R 177 "
      ideal   model   delta    sigma   weight residual
     111.14  123.07  -11.93 1.08e+00 8.57e-01 1.22e+02
  angle pdb=" C   TYR S 223 "
        pdb=" N   PRO S 224 "
        pdb=" CD  PRO S 224 "
      ideal   model   delta    sigma   weight residual
     120.60  137.91  -17.31 2.20e+00 2.07e-01 6.19e+01
  angle pdb=" N   TYR R 397 "
        pdb=" CA  TYR R 397 "
        pdb=" C   TYR R 397 "
      ideal   model   delta    sigma   weight residual
     111.36  119.69   -8.33 1.09e+00 8.42e-01 5.84e+01
  angle pdb=" N   LEU R 193 "
        pdb=" CA  LEU R 193 "
        pdb=" C   LEU R 193 "
      ideal   model   delta    sigma   weight residual
     114.39  103.36   11.03 1.45e+00 4.76e-01 5.78e+01
  angle pdb=" N   LEU S 225 "
        pdb=" CA  LEU S 225 "
        pdb=" C   LEU S 225 "
      ideal   model   delta    sigma   weight residual
     111.17  121.84  -10.67 1.41e+00 5.03e-01 5.73e+01
  ... (remaining 11743 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.03: 4939
       17.03 -    34.07: 177
       34.07 -    51.10: 34
       51.10 -    68.14: 9
       68.14 -    85.17: 2
  Dihedral angle restraints: 5161
    sinusoidal: 1911
      harmonic: 3250
  Sorted by residual:
  dihedral pdb=" N   TYR S 178 "
           pdb=" C   TYR S 178 "
           pdb=" CA  TYR S 178 "
           pdb=" CB  TYR S 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  143.79  -20.99     0      2.50e+00 1.60e-01 7.05e+01
  dihedral pdb=" C   TYR S 178 "
           pdb=" N   TYR S 178 "
           pdb=" CA  TYR S 178 "
           pdb=" CB  TYR S 178 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -142.31   19.71     0      2.50e+00 1.60e-01 6.21e+01
  dihedral pdb=" C   TRP R 241 "
           pdb=" N   TRP R 241 "
           pdb=" CA  TRP R 241 "
           pdb=" CB  TRP R 241 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.20   16.60     0      2.50e+00 1.60e-01 4.41e+01
  ... (remaining 5158 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.187: 1319
       0.187 -    0.374: 42
       0.374 -    0.561: 7
       0.561 -    0.749: 1
       0.749 -    0.936: 1
  Chirality restraints: 1370
  Sorted by residual:
  chirality pdb=" CA  TYR S 178 "
            pdb=" N   TYR S 178 "
            pdb=" C   TYR S 178 "
            pdb=" CB  TYR S 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.57    0.94 2.00e-01 2.50e+01 2.19e+01
  chirality pdb=" CA  TRP R 241 "
            pdb=" N   TRP R 241 "
            pdb=" C   TRP R 241 "
            pdb=" CB  TRP R 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.83    0.68 2.00e-01 2.50e+01 1.16e+01
  chirality pdb=" CA  LEU S 225 "
            pdb=" N   LEU S 225 "
            pdb=" C   LEU S 225 "
            pdb=" CB  LEU S 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.56e+00
  ... (remaining 1367 not shown)

  Planarity restraints: 1463
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP S 111 "   -0.032 2.00e-02 2.50e+03   2.56e-02 1.64e+01
        pdb=" CG  TRP S 111 "    0.068 2.00e-02 2.50e+03
        pdb=" CD1 TRP S 111 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TRP S 111 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP S 111 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP S 111 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP S 111 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP S 111 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP S 111 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP S 111 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO R 394 "    0.020 2.00e-02 2.50e+03   4.04e-02 1.63e+01
        pdb=" C   PRO R 394 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   PRO R 394 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ILE R 395 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 256 "    0.020 2.00e-02 2.50e+03   3.97e-02 1.57e+01
        pdb=" CG  ASN A 256 "   -0.069 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 256 "    0.026 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 256 "    0.023 2.00e-02 2.50e+03
  ... (remaining 1460 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.46: 51
        2.46 -     3.07: 5955
        3.07 -     3.68: 11467
        3.68 -     4.29: 16674
        4.29 -     4.90: 28813
  Nonbonded interactions: 62960
  Sorted by model distance:
  nonbonded pdb=" CE  MET R 371 "
            pdb=" CB  ILE R 375 "
     model   vdw
     1.855 3.890
  nonbonded pdb=" O   ASP B  66 "
            pdb=" OG  SER B  67 "
     model   vdw
     1.962 3.040
  nonbonded pdb=" O   ASP B  38 "
            pdb=" OD1 ASP B  38 "
     model   vdw
     1.981 3.040
  nonbonded pdb=" O   HIS S 220 "
            pdb=" ND1 HIS S 220 "
     model   vdw
     2.011 3.120
  nonbonded pdb=" CD1 ILE S 126 "
            pdb=" OE2 GLU S 222 "
     model   vdw
     2.077 3.460
  ... (remaining 62955 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:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     22.660
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
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      :  0.011   0.241   8636  Z= 0.767
  Angle     :  1.400  17.310  11748  Z= 0.876
  Chirality :  0.091   0.936   1370
  Planarity :  0.008   0.075   1463
  Dihedral  :  9.763  85.169   3058
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  2.88 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.38 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.23), residues: 1101
  helix: -1.09 (0.27), residues: 320
  sheet: -1.55 (0.30), residues: 253
  loop : -1.65 (0.24), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.068   0.005   TRP S 111 
 HIS   0.011   0.003   HIS R 143 
 PHE   0.030   0.004   PHE A 196 
 TYR   0.049   0.005   TYR A 287 
 ARG   0.010   0.001   ARG B 314 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 224
  time to evaluate  : 0.941 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7919 (tt0) cc_final: 0.7571 (tt0)
REVERT: B   13 GLN cc_start: 0.7174 (mt0) cc_final: 0.6929 (tt0)
REVERT: C   18 GLN cc_start: 0.7284 (tp-100) cc_final: 0.7065 (tp-100)
REVERT: R  186 ARG cc_start: 0.6786 (mtm180) cc_final: 0.5387 (ttt180)
REVERT: R  347 LEU cc_start: 0.8691 (tp) cc_final: 0.8428 (tt)
  outliers start: 7
  outliers final: 4
  residues processed: 229
  average time/residue: 1.1335
  time to fit residues: 277.2770
Evaluate side-chains
  140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 136
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  264 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   chunk 63 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 255 ASN
A 311 ASN
B  91 HIS
B 220 GLN
B 259 GLN
R 154 HIS
R 178 HIS
R 304 HIS
S   3 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.145741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.115440 restraints weight = 11755.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.94
r_work: 0.3536 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8636  Z= 0.255
  Angle     :  0.679  10.366  11748  Z= 0.359
  Chirality :  0.045   0.168   1370
  Planarity :  0.005   0.044   1463
  Dihedral  :  7.300  69.533   1359
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 13.57 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.24), residues: 1101
  helix: -0.38 (0.28), residues: 344
  sheet: -0.97 (0.29), residues: 272
  loop : -1.75 (0.25), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 332 
 HIS   0.006   0.001   HIS R 143 
 PHE   0.017   0.002   PHE R 289 
 TYR   0.024   0.002   TYR S 178 
 ARG   0.007   0.001   ARG C  62 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 140
  time to evaluate  : 0.909 
Fit side-chains
REVERT: A  333 GLN cc_start: 0.8361 (tp40) cc_final: 0.7695 (tm-30)
REVERT: B   13 GLN cc_start: 0.6874 (mt0) cc_final: 0.6654 (tt0)
REVERT: B  217 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8198 (pmm)
REVERT: B  227 SER cc_start: 0.8861 (m) cc_final: 0.8163 (t)
REVERT: B  292 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8313 (m-80)
REVERT: C   18 GLN cc_start: 0.6968 (tp-100) cc_final: 0.6725 (tp-100)
REVERT: C   63 GLU cc_start: 0.6512 (tp30) cc_final: 0.6285 (tp30)
REVERT: R  308 MET cc_start: 0.6678 (mmp) cc_final: 0.5757 (tmt)
REVERT: R  309 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7451 (pt)
REVERT: R  353 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7022 (tp)
REVERT: S   60 TYR cc_start: 0.9149 (m-80) cc_final: 0.8948 (m-80)
  outliers start: 32
  outliers final: 14
  residues processed: 162
  average time/residue: 1.0302
  time to fit residues: 179.6426
Evaluate side-chains
  138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain R residue  137 VAL
Chi-restraints excluded: chain R residue  212 ILE
Chi-restraints excluded: chain R residue  264 CYS
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  291 VAL
Chi-restraints excluded: chain R residue  309 ILE
Chi-restraints excluded: chain R residue  353 ILE
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 57 optimal weight:    7.9990
   chunk 97 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 178 HIS
S   3 GLN
S 113 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.144628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.113924 restraints weight = 11954.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 2.99
r_work: 0.3525 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8636  Z= 0.190
  Angle     :  0.584  10.807  11748  Z= 0.307
  Chirality :  0.042   0.204   1370
  Planarity :  0.004   0.044   1463
  Dihedral  :  6.815  67.900   1355
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 14.29 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.24), residues: 1101
  helix: -0.01 (0.29), residues: 352
  sheet: -0.62 (0.30), residues: 273
  loop : -1.54 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 143 
 PHE   0.013   0.001   PHE R 289 
 TYR   0.020   0.001   TYR S 178 
 ARG   0.005   0.000   ARG B  42 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 133
  time to evaluate  : 0.860 
Fit side-chains
REVERT: A  276 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8475 (pp20)
REVERT: A  308 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8126 (mt-10)
REVERT: A  333 GLN cc_start: 0.8348 (tp40) cc_final: 0.7704 (tm-30)
REVERT: B  217 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8187 (pmm)
REVERT: B  227 SER cc_start: 0.8846 (m) cc_final: 0.8148 (t)
REVERT: B  292 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8270 (m-10)
REVERT: C   21 MET cc_start: 0.8281 (tpp) cc_final: 0.8004 (mpp)
REVERT: C   58 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7603 (pm20)
REVERT: C   63 GLU cc_start: 0.6584 (tp30) cc_final: 0.6247 (tp30)
REVERT: R  308 MET cc_start: 0.6552 (mmp) cc_final: 0.5662 (tmt)
REVERT: S   84 THR cc_start: 0.7998 (m) cc_final: 0.7594 (p)
  outliers start: 35
  outliers final: 17
  residues processed: 153
  average time/residue: 0.9563
  time to fit residues: 158.3202
Evaluate side-chains
  144 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain R residue  193 LEU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  291 VAL
Chi-restraints excluded: chain R residue  339 ILE
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 38 optimal weight:    7.9990
   chunk 47 optimal weight:    0.7980
   chunk 62 optimal weight:    9.9990
   chunk 102 optimal weight:    0.0050
   chunk 86 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 5 optimal weight:    0.4980
   chunk 71 optimal weight:   10.0000
   overall best weight:    0.8396

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 178 HIS
S   3 GLN
S 182 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.147706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.117288 restraints weight = 11886.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 2.95
r_work: 0.3540 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8636  Z= 0.143
  Angle     :  0.531  10.904  11748  Z= 0.277
  Chirality :  0.040   0.213   1370
  Planarity :  0.003   0.046   1463
  Dihedral  :  6.348  64.816   1354
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 16.09 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.25), residues: 1101
  helix:  0.29 (0.29), residues: 356
  sheet: -0.39 (0.30), residues: 277
  loop : -1.38 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 279 
 HIS   0.005   0.001   HIS R 143 
 PHE   0.024   0.001   PHE R 237 
 TYR   0.013   0.001   TYR S 215 
 ARG   0.004   0.000   ARG B  42 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 136
  time to evaluate  : 0.974 
Fit side-chains
REVERT: A   46 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8165 (mttp)
REVERT: A  276 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8587 (pp20)
REVERT: A  308 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8030 (mt-10)
REVERT: A  333 GLN cc_start: 0.8420 (tp40) cc_final: 0.7822 (tm-30)
REVERT: B  217 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8244 (pmm)
REVERT: B  292 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8367 (m-10)
REVERT: C   58 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7666 (pm20)
REVERT: C   63 GLU cc_start: 0.6641 (tp30) cc_final: 0.6340 (tp30)
REVERT: R  308 MET cc_start: 0.6395 (mmp) cc_final: 0.5709 (tmt)
REVERT: S   84 THR cc_start: 0.8060 (m) cc_final: 0.7722 (p)
  outliers start: 34
  outliers final: 15
  residues processed: 154
  average time/residue: 1.0103
  time to fit residues: 167.6392
Evaluate side-chains
  141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain R residue  193 LEU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  291 VAL
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0980
   chunk 53 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    0.0170
   chunk 74 optimal weight:    0.0050
   chunk 59 optimal weight:    0.0980
   chunk 38 optimal weight:    7.9990
   chunk 67 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    0.6434

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 178 HIS
S   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.148933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.118901 restraints weight = 11785.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 2.94
r_work: 0.3575 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.3567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8636  Z= 0.127
  Angle     :  0.513  12.209  11748  Z= 0.267
  Chirality :  0.040   0.251   1370
  Planarity :  0.003   0.045   1463
  Dihedral  :  6.166  62.996   1354
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.89 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.25), residues: 1101
  helix:  0.64 (0.29), residues: 353
  sheet: -0.24 (0.31), residues: 274
  loop : -1.22 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 279 
 HIS   0.004   0.001   HIS R 143 
 PHE   0.027   0.001   PHE R 237 
 TYR   0.011   0.001   TYR S 178 
 ARG   0.009   0.000   ARG A  24 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A   46 LYS cc_start: 0.8445 (mtpt) cc_final: 0.8129 (mttp)
REVERT: A  276 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8584 (pp20)
REVERT: A  308 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7988 (mt-10)
REVERT: A  333 GLN cc_start: 0.8453 (tp40) cc_final: 0.7850 (tm-30)
REVERT: B  214 ARG cc_start: 0.8338 (mtt90) cc_final: 0.8103 (mtt180)
REVERT: B  217 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8187 (pmm)
REVERT: C   21 MET cc_start: 0.8361 (tpp) cc_final: 0.8006 (mpp)
REVERT: C   58 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7594 (pm20)
REVERT: R  181 HIS cc_start: 0.7236 (t70) cc_final: 0.5960 (p90)
REVERT: R  308 MET cc_start: 0.6347 (mmp) cc_final: 0.5644 (tmt)
REVERT: R  365 TYR cc_start: 0.7288 (t80) cc_final: 0.7056 (t80)
REVERT: S   84 THR cc_start: 0.8066 (m) cc_final: 0.7778 (p)
  outliers start: 29
  outliers final: 11
  residues processed: 165
  average time/residue: 0.9283
  time to fit residues: 165.8866
Evaluate side-chains
  149 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain R residue  193 LEU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  291 VAL
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 81 optimal weight:    8.9990
   chunk 32 optimal weight:    7.9990
   chunk 94 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 91 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 74 optimal weight:    0.0020
   chunk 57 optimal weight:    0.0980
   chunk 12 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.9392

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 178 HIS
S   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.147363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.117017 restraints weight = 11860.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 3.00
r_work: 0.3541 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.3694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8636  Z= 0.146
  Angle     :  0.535  11.824  11748  Z= 0.275
  Chirality :  0.040   0.248   1370
  Planarity :  0.003   0.044   1463
  Dihedral  :  6.004  61.899   1352
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 19.45 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.25), residues: 1101
  helix:  0.84 (0.29), residues: 353
  sheet: -0.05 (0.31), residues: 272
  loop : -1.21 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 279 
 HIS   0.004   0.001   HIS R 143 
 PHE   0.021   0.001   PHE R 237 
 TYR   0.014   0.001   TYR S 178 
 ARG   0.007   0.000   ARG A  24 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 136
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8207 (mttp)
REVERT: A  308 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7962 (mt-10)
REVERT: A  333 GLN cc_start: 0.8506 (tp40) cc_final: 0.7885 (tm-30)
REVERT: B  217 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8212 (pmm)
REVERT: C   21 MET cc_start: 0.8399 (tpp) cc_final: 0.8116 (mpp)
REVERT: C   58 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7654 (pm20)
REVERT: R  181 HIS cc_start: 0.7265 (t70) cc_final: 0.6001 (p90)
REVERT: R  353 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6973 (tp)
REVERT: R  365 TYR cc_start: 0.7356 (t80) cc_final: 0.7083 (t80)
REVERT: S    2 VAL cc_start: 0.7555 (OUTLIER) cc_final: 0.7244 (p)
REVERT: S   84 THR cc_start: 0.8100 (m) cc_final: 0.7822 (p)
  outliers start: 29
  outliers final: 17
  residues processed: 154
  average time/residue: 0.9972
  time to fit residues: 165.6383
Evaluate side-chains
  148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain R residue  193 LEU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  291 VAL
Chi-restraints excluded: chain R residue  353 ILE
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 12 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 101 optimal weight:    6.9990
   chunk 43 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   chunk 5 optimal weight:    8.9990
   chunk 81 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 21 optimal weight:    0.3980
   overall best weight:    2.8788

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 178 HIS
R 389 ASN
S   3 GLN
S 182 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.140802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.110406 restraints weight = 12096.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 2.95
r_work: 0.3470 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   8636  Z= 0.320
  Angle     :  0.634  11.941  11748  Z= 0.333
  Chirality :  0.044   0.205   1370
  Planarity :  0.004   0.046   1463
  Dihedral  :  6.561  63.526   1352
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 19.81 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.25), residues: 1101
  helix:  0.70 (0.29), residues: 356
  sheet: -0.30 (0.31), residues: 282
  loop : -1.35 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP S  47 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.020   0.002   PHE B 335 
 TYR   0.033   0.002   TYR S 178 
 ARG   0.008   0.001   ARG A  24 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 ILE cc_start: 0.7958 (tt) cc_final: 0.7753 (tt)
REVERT: A  308 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8086 (mt-10)
REVERT: A  316 THR cc_start: 0.8742 (m) cc_final: 0.8457 (p)
REVERT: A  333 GLN cc_start: 0.8419 (tp40) cc_final: 0.7826 (tm-30)
REVERT: B  217 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8119 (pmm)
REVERT: C   11 GLN cc_start: 0.6888 (tm-30) cc_final: 0.6310 (tm-30)
REVERT: C   32 LYS cc_start: 0.7355 (ttpt) cc_final: 0.7066 (tttp)
REVERT: C   58 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7559 (pm20)
REVERT: S    2 VAL cc_start: 0.7841 (OUTLIER) cc_final: 0.7623 (t)
REVERT: S   84 THR cc_start: 0.7978 (m) cc_final: 0.7563 (p)
REVERT: S  128 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.7699 (mmm)
REVERT: S  189 ASP cc_start: 0.7739 (t0) cc_final: 0.7335 (m-30)
  outliers start: 33
  outliers final: 21
  residues processed: 147
  average time/residue: 1.1138
  time to fit residues: 175.8106
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain R residue  137 VAL
Chi-restraints excluded: chain R residue  212 ILE
Chi-restraints excluded: chain R residue  291 VAL
Chi-restraints excluded: chain R residue  300 LYS
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  128 MET
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 82 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   chunk 15 optimal weight:    0.0980
   chunk 21 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0470
   chunk 75 optimal weight:    0.1980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.6480

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S   3 GLN
S 182 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.140332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.108084 restraints weight = 11943.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 3.02
r_work: 0.3308 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.3950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8636  Z= 0.137
  Angle     :  0.536   9.280  11748  Z= 0.278
  Chirality :  0.040   0.202   1370
  Planarity :  0.003   0.043   1463
  Dihedral  :  5.907  59.120   1352
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 22.45 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.25), residues: 1101
  helix:  0.91 (0.29), residues: 357
  sheet: -0.13 (0.30), residues: 279
  loop : -1.15 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 279 
 HIS   0.005   0.001   HIS R 143 
 PHE   0.024   0.001   PHE R 237 
 TYR   0.009   0.001   TYR S  60 
 ARG   0.009   0.000   ARG A  24 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.8511 (mtpt) cc_final: 0.8308 (mttp)
REVERT: A  316 THR cc_start: 0.8823 (m) cc_final: 0.8564 (p)
REVERT: A  333 GLN cc_start: 0.8613 (tp40) cc_final: 0.8032 (tm-30)
REVERT: B  217 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8397 (pmm)
REVERT: B  234 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8036 (m-80)
REVERT: C   21 MET cc_start: 0.8480 (tpp) cc_final: 0.8162 (mpp)
REVERT: C   58 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7743 (pm20)
REVERT: R  409 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6222 (ttp80)
REVERT: S    2 VAL cc_start: 0.7648 (OUTLIER) cc_final: 0.7301 (p)
REVERT: S   84 THR cc_start: 0.8322 (m) cc_final: 0.8054 (p)
REVERT: S  189 ASP cc_start: 0.7820 (t0) cc_final: 0.7440 (m-30)
  outliers start: 18
  outliers final: 9
  residues processed: 142
  average time/residue: 1.0712
  time to fit residues: 163.4524
Evaluate side-chains
  136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain R residue  291 VAL
Chi-restraints excluded: chain R residue  339 ILE
Chi-restraints excluded: chain R residue  409 ARG
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  137 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 68 optimal weight:    7.9990
   chunk 83 optimal weight:    4.9990
   chunk 107 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 70 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 75 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S   3 GLN
S 182 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.140843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.110207 restraints weight = 12119.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 2.99
r_work: 0.3431 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   8636  Z= 0.302
  Angle     :  0.622  13.235  11748  Z= 0.325
  Chirality :  0.043   0.210   1370
  Planarity :  0.004   0.046   1463
  Dihedral  :  6.337  60.880   1352
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 22.45 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.25), residues: 1101
  helix:  0.84 (0.29), residues: 356
  sheet: -0.24 (0.31), residues: 281
  loop : -1.35 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP S  47 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.021   0.002   PHE B 335 
 TYR   0.028   0.002   TYR S 178 
 ARG   0.009   0.001   ARG A  24 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.894 
Fit side-chains
REVERT: A   46 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8213 (mttp)
REVERT: A  316 THR cc_start: 0.8784 (m) cc_final: 0.8514 (p)
REVERT: A  333 GLN cc_start: 0.8459 (tp40) cc_final: 0.7877 (tm-30)
REVERT: B  217 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8188 (pmm)
REVERT: C   11 GLN cc_start: 0.6971 (tm-30) cc_final: 0.6298 (tm-30)
REVERT: C   21 MET cc_start: 0.8382 (tpp) cc_final: 0.8114 (mpp)
REVERT: C   32 LYS cc_start: 0.7477 (ttpt) cc_final: 0.7205 (tttp)
REVERT: C   58 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7585 (pm20)
REVERT: S   84 THR cc_start: 0.8134 (m) cc_final: 0.7694 (p)
REVERT: S  189 ASP cc_start: 0.7854 (t0) cc_final: 0.7409 (m-30)
  outliers start: 17
  outliers final: 14
  residues processed: 135
  average time/residue: 1.0518
  time to fit residues: 152.5971
Evaluate side-chains
  138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  291 VAL
Chi-restraints excluded: chain R residue  339 ILE
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 46 optimal weight:    0.8980
   chunk 4 optimal weight:    7.9990
   chunk 102 optimal weight:    7.9990
   chunk 92 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.146336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.113981 restraints weight = 11925.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.92
r_work: 0.3437 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.3921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8636  Z= 0.252
  Angle     :  0.601   8.959  11748  Z= 0.314
  Chirality :  0.043   0.203   1370
  Planarity :  0.004   0.045   1463
  Dihedral  :  6.343  59.809   1352
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 22.09 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.25), residues: 1101
  helix:  0.88 (0.29), residues: 355
  sheet: -0.23 (0.30), residues: 282
  loop : -1.39 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP S  47 
 HIS   0.005   0.001   HIS R 143 
 PHE   0.034   0.002   PHE R 289 
 TYR   0.022   0.002   TYR S 178 
 ARG   0.009   0.000   ARG A  24 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8189 (mttt)
REVERT: A  316 THR cc_start: 0.8809 (m) cc_final: 0.8558 (p)
REVERT: A  333 GLN cc_start: 0.8474 (tp40) cc_final: 0.7887 (tm-30)
REVERT: B  217 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8193 (pmm)
REVERT: C   11 GLN cc_start: 0.6997 (tm-30) cc_final: 0.6309 (tm-30)
REVERT: C   21 MET cc_start: 0.8387 (tpp) cc_final: 0.8118 (mpp)
REVERT: C   32 LYS cc_start: 0.7502 (ttpt) cc_final: 0.7182 (tttm)
REVERT: C   58 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7609 (pm20)
REVERT: S   84 THR cc_start: 0.8211 (m) cc_final: 0.7805 (p)
REVERT: S  189 ASP cc_start: 0.7890 (t0) cc_final: 0.7454 (m-30)
  outliers start: 16
  outliers final: 14
  residues processed: 133
  average time/residue: 1.0954
  time to fit residues: 156.5064
Evaluate side-chains
  137 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  291 VAL
Chi-restraints excluded: chain R residue  339 ILE
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 72 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0470
   chunk 69 optimal weight:    6.9990
   chunk 32 optimal weight:    7.9990
   chunk 79 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.9882

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S   3 GLN
S 182 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.138853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.106554 restraints weight = 11973.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 3.02
r_work: 0.3287 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.4091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8636  Z= 0.160
  Angle     :  0.568  14.177  11748  Z= 0.293
  Chirality :  0.041   0.206   1370
  Planarity :  0.003   0.043   1463
  Dihedral  :  5.907  58.335   1352
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 22.57 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.26), residues: 1101
  helix:  1.08 (0.29), residues: 356
  sheet: -0.13 (0.31), residues: 279
  loop : -1.24 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 279 
 HIS   0.005   0.001   HIS R 143 
 PHE   0.035   0.001   PHE R 289 
 TYR   0.011   0.001   TYR S 178 
 ARG   0.009   0.000   ARG A  24 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5582.40 seconds
wall clock time: 99 minutes 14.26 seconds (5954.26 seconds total)